Inhibitors of menin-mll interaction

ABSTRACT

Disclosed herein are heterocyclic compounds that inhibit the binding of menin and MLL or MLL fusion proteins. Also described are specific inhibitors of menin-MLL interaction. Also disclosed are pharmaceutical compositions that include the compounds. Methods of using the menin-MLL inhibitors are disclosed, alone or in combination with other therapeutic agents, for the treatment of autoimmune diseases or conditions, heteroimmune diseases or conditions, cancer, including lymphoma, leukemia and other diseases or conditions dependent on menin-MLL interaction.

FIELD OF THE INVENTION

Described herein are compounds, methods of making such compounds, pharmaceutical compositions and medicaments containing such compounds, and methods of using such compounds and compositions to inhibit the activity of menin-MLL. (And may also serve as an anti-tumor agent through off-target activity by impacting other protein-protein interactions as well as kinases.)

BACKGROUND OF THE INVENTION

The Histone-lysine A-methyltransferase 2 (KMT2) family of proteins, which currently consists of at least 5 members, methylate lysine 4 on the histone H3 tails at important regulatory regions in the genome and thereby impart crucial functions through the modulation of chromatin structures and DNA accessibility (Morera, Lübbert, and Jung., Clin. Epigenetics, 8, 57-(2016)). These enzymes are known to play an important role in the regulation of gene expression during early development and hematopoiesis (Rao & Dou., Nat. Rev. Cancer, 15, 334-346 (2015)).

The human KMT2 family was initially named the mixed-lineage leukaemia (MLL) family, owing to the role of the first-found member in this disease, KMT2A which is still commonly referred to as MLL1 or MLL in routine clinical practice.

KMT2A (MLL1) is frequently found to be cytogenetically targeted in several types of leukemia (e.g. ALL and AML), and in those cases where balanced chromosomal translocations are found, these typically target KMT2A (MLL1) and one of over 80 translocation partner genes that have been described to date (Winters and Bernt, Front. Pediatr., 5, 4 (2017)). These chromosomal anomalies often result in the formation of fusion genes that encode fusion proteins which are believed to be causally related to the onset and/or progression of the disease.

SUMMARY OF THE INVENTION

Described herein are inhibitors of menin-MLL interaction. Also described herein are specific heterocyclic inhibitors of menin-MLL or MLL fusion proteins interaction.

Also described herein are methods for synthesizing such inhibitors, methods for using such inhibitors in the treatment of diseases (including diseases wherein inhibition of menin-MLL interaction provides therapeutic benefit to a patient having the disease). Further described are pharmaceutical compositions that include an inhibitor of menin-MLL interaction. Specifically, described herein are compounds and methods of use thereof to inhibit interaction of menin with MLL oncoproteins (e.g., MLL1, MLL2, MLL-fusion oncoproteins).

Thus, in some embodiments, the present invention provides methods for preventing, treating or ameliorating in a mammal a disease or condition that is causally related to the aberrant activity of a menin-MLL interaction in vivo, which comprises administering to the mammal an effective disease-treating or condition-treating amount of a compound according to Formula (I) having the structure:

-   -   or a pharmaceutically acceptable salt thereof,     -   wherein:         A is O, or N(R^(6a));     -   Cy is substituted or unsubstituted

-   -   Q is —N(H)—, —O—, or —S—; Q′ is N, or C(H);     -   Z is —CR^(5a)═ or —N═;     -   one of X and Y is —NR^(3a)—; and the other is —C(R^(3b))₂—,         —NR^(3b)—, or —O—;     -   R¹ is an optionally substituted group selected from C₁₋₆ alkyl,         C₃₋₇ cycloalkyl, phenyl, an 8-10 membered bicyclic aryl ring, a         4-7 membered heterocycloalkyl ring having 1-2 heteroatoms         independently selected from nitrogen, oxygen, or sulfur, and a         5-6 membered heteroaryl ring having 1-4 heteroatoms         independently selected from nitrogen, oxygen, or sulfur;     -   R² is H, C₁₋₆ alkyl, C₁₋₆haloalkyl, halo, or CN;     -   each R^(3a), and R^(3b) is independently H or C₁₋₆ alkyl;     -   each R⁴ is independently H, halo, CN, OR, —N(R)₂, —C(O)N(R)₂,         —NRC(O)R, —SO₂R, —C(O)R, —CO₂R, or an optionally substituted         group selected from C₁₋₆ alkyl, C₃₋₇ cycloalkyl, a 4-7 membered         heterocycloalkyl ring having 1-2 heteroatoms independently         selected from nitrogen, oxygen, or sulfur, phenyl, an 8-10         membered bicyclic aryl ring, and a 5-6 membered heteroaryl ring         having 1-4 heteroatoms independently selected from nitrogen,         oxygen, or sulfur;     -   each R is independently H, or an optionally substituted group         selected from C₁₋₆ aliphatic, phenyl, an 8-10 membered bicyclic         aryl ring, a 4-7 membered saturated or partially unsaturated         heterocyclic ring having 1-2 heteroatoms independently selected         from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl         ring having 1-4 heteroatoms independently selected from         nitrogen, oxygen, or sulfur, or:     -   two R groups on the same nitrogen are taken together with their         intervening atoms to form a 4-7 membered saturated, partially         unsaturated, or heteroaryl ring having 0-3 heteroatoms, in         addition to the nitrogen, independently selected from nitrogen,         oxygen, or sulfur;     -   R^(5a) is H, C₁₋₆ alkyl, C₁₋₆haloalkyl, halo, or CN;     -   R^(6a) is H or and C₁₋₆ alkyl; and n is 1, 2, 3, or 4.

In some embodiments, the present invention provides a compound according to Formula (I) having the structure:

-   -   or a pharmaceutically acceptable salt thereof,     -   wherein:         A is O, or N(R^(6a));     -   Cy is substituted or unsubstituted

-   -   Q is —N(H)—, —O—, or —S—; Q′ is N, or C(H);     -   Z is —CR^(5a)═ or —N═;     -   one of X and Y is —NR^(3a)—; and the other is —C(R^(3b))₂—,         —NR^(3b)—, or —O—;     -   R¹ is an optionally substituted group selected from C₁₋₆ alkyl,         C₃₋₇ cycloalkyl, phenyl, an 8-10 membered bicyclic aryl ring, a         4-7 membered heterocycloalkyl ring having 1-2 heteroatoms         independently selected from nitrogen, oxygen, or sulfur, and a         5-6 membered heteroaryl ring having 1-4 heteroatoms         independently selected from nitrogen, oxygen, or sulfur;     -   R² is H, C₁₋₆ alkyl, C₁₋₆haloalkyl, halo, or CN;     -   each R^(3a), and R^(3b) is independently H or C₁₋₆ alkyl;     -   each R⁴ is independently H, halo, CN, OR, —N(R)₂, —C(O)N(R)₂,         —NRC(O)R, —SO₂R, —C(O)R, —CO₂R, or an optionally substituted         group selected from C₁₋₆ alkyl, C₃₋₇ cycloalkyl, a 4-7 membered         heterocycloalkyl ring having 1-2 heteroatoms independently         selected from nitrogen, oxygen, or sulfur, phenyl, an 8-10         membered bicyclic aryl ring, and a 5-6 membered heteroaryl ring         having 1-4 heteroatoms independently selected from nitrogen,         oxygen, or sulfur;     -   each R is independently H, or an optionally substituted group         selected from C₁₋₆ aliphatic, phenyl, an 8-10 membered bicyclic         aryl ring, a 4-7 membered saturated or partially unsaturated         heterocyclic ring having 1-2 heteroatoms independently selected         from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl         ring having 1-4 heteroatoms independently selected from         nitrogen, oxygen, or sulfur, or:     -   two R groups on the same nitrogen are taken together with their         intervening atoms to form a 4-7 membered saturated, partially         unsaturated, or heteroaryl ring having 0-3 heteroatoms, in         addition to the nitrogen, independently selected from nitrogen,         oxygen, or sulfur;     -   R^(5a) is H, C₁₋₆ alkyl, C₁₋₆haloalkyl, halo, or CN;     -   R^(6a) is H or and C₁₋₆ alkyl; and     -   n is 1, 2, 3, or 4.

In some embodiments, X is —N(H)— and Y is —NH—, —C(H)₂— or O. In some embodiments, each of X and Y is —N(H)—.

In some embodiments, Cy is substituted or unsubstituted

In some embodiments, Q is —N(H)—.

In some embodiments, Z is —C(H)═.

In some embodiments, Cy is unsubstituted. In some embodiments, Cy is substituted. In some embodiments, Cy is substituted with phenyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl. In some embodiments, Cy is phenyl substituted with halo, CN, C₁₋₆alkyl or alkoxy. In some embodiments, Cy is substituted with pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, or thiadiazolyl. In some embodiments, Cy is substituted with pyrrolyl, pyrazolyl, or imidazolyl. In some embodiments, Cy is substituted with methylimidazolyl.

In some embodiments, each R⁴ is independently H, halo, hydroxyl, CN, substituted or unsubstituted alkyl, substituted or unsubstituted amino, substituted or unsubstituted alkoxy, substituted or unsubstituted amido, substituted or unsubstituted sulfonyl, substituted or unsubstituted carboxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

In some embodiments, R¹ is substituted or unsubstituted cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl.

In some embodiments, R¹ is heteroaryl. In some embodiments, R¹ is 3-pyridyl. In some embodiments, R¹ is 4-pyridyl.

In some embodiments, R² is H.

In some embodiments, the active site is a cavity in which the compound or the moiety binds to the MLL site on the menin. In some embodiments, the active site is MEN1 at the MLL binding site.

In some embodiments, the disease or condition is an autoimmune disease, a heteroimmune disease, a cancer, mastocytosis, osteoporosis or bone resorption disorder, or an inflammatory disease.

In some embodiments, the compounds of the invention may also serve as an anti-tumor agents through off-target activity by impacting other protein-protein interactions as well as kinases.

In some embodiments, the compound is according to formula (VIIa′), (VIIb′), (VIIe′) or (VIId′):

-   -   or a pharmaceutically acceptable salt thereof     -   wherein:     -   R¹ is as described herein; and R⁷ is an optionally substituted         group selected from a 4-7 membered heterocycloalkyl ring having         1-2 heteroatoms independently selected from nitrogen, oxygen, or         sulfur, and a 5-6 membered heteroaryl ring having 1-4         heteroatoms independently selected from nitrogen, oxygen, or         sulfur.

In some embodiments, R¹ is heteroaryl. In some embodiments, R¹ is 3-pyridyl. In some embodiments, R¹ is 4-pyridyl.

In some embodiments, R⁷ is piperidinyl, piperizanyl, or morpholinyl. In some embodiments, R⁷ is imidazolyl, unsubstituted or substituted with methyl.

In some embodiments, the present invention provides pharmaceutical compositions comprising a therapeutically effective amount of a compound of Formula (I) and a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition comprising the compound of Formula (I) is formulated for a route of administration selected from oral administration, parenteral administration, buccal administration, nasal administration, topical administration, or rectal administration. In some embodiments, the present invention provides methods for treating an autoimmune disease or condition comprising administering to a patient in need a therapeutically effective amount of a compound of Formula (I). In some embodiments the autoimmune disease is selected from rheumatoid arthritis or lupus. In some embodiments, the present invention provides a method for treating a heteroimmune disease or condition comprising administering to a patient in need a therapeutically effective amount of a compound of Formula (I). In some embodiments the present invention provides a method for treating a cancer comprising administering to a patient in need a therapeutically effective amount of a compound of Formula (I). In some embodiments, the cancer is a myeloid line of blood cells. In some embodiments, the cancer is a lymphoid line of blood cell. In some embodiments, the cancer is a B-cell proliferative disorder. In some embodiments, the cancer is a lymphoid line of blood cells.

In some embodiments the myeloid line of blood cells is acute myeloid leukemia. In some embodiments the lymphoid line of blood cells is acute lymphoblastic leukemia. In some embodiments the B-cell proliferative disorder is diffuse large B cell lymphoma, follicular lymphoma or chronic lymphocytic leukemia. In some embodiments the cancer (soft tissue) is glioblastoma and pancreatic cancer. In some embodiments the cancer is renal cell carcinoma.

In some embodiments, the present invention provides a method for treating mastocytosis comprising administering to a patient in need a therapeutically effective amount of a compound of Formula (I).

In some embodiments, the present invention provides a method for treating osteoporosis or bone resorption disorders comprising administering to a patient in need a therapeutically effective amount of a compound of Formula (I).

In some embodiments, the present invention provides a method for treating an inflammatory disease or condition comprising administering to a patient in need a therapeutically effective amount of a compound of Formula (I).

Any combination of the groups described above for the various variables is contemplated herein. It is understood that substituents and substitution patterns on the compounds provided herein can be selected by one of ordinary skill in the art to provide compounds that are chemically stable and that can be synthesized by techniques known in the art, as well as those set forth herein.

In some embodiments, the present invention provides pharmaceutical compositions, which include a therapeutically effective amount of at least one of any of the compounds herein, or a pharmaceutically acceptable salt, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate. In certain embodiments, compositions provided herein further include a pharmaceutically acceptable diluent, excipient and/or binder.

Pharmaceutical compositions formulated for administration by an appropriate route and means containing effective concentrations of one or more of the compounds provided herein, or pharmaceutically effective derivatives thereof, that deliver amounts effective for the treatment, prevention, or amelioration of one or more symptoms of diseases, disorders or conditions that are modulated or otherwise affected by Menin-MLL activity, or in which Menin-MLL activity is implicated, are provided. The effective amounts and concentrations are effective for ameliorating any of the symptoms of any of the diseases, disorders or conditions disclosed herein.

In certain embodiments, provided herein is a pharmaceutical composition containing: i) a physiologically acceptable carrier, diluent, and/or excipient; and ii) one or more compounds provided herein.

In some embodiments, provided herein are methods for treating a patient by administering a compound provided herein. In some embodiments, provided herein is a method of inhibiting the activity of Menin-MLL, or of treating a disease, disorder, or condition, which would benefit from inhibition of Menin-MLL activity, in a patient, which includes administering to the patient a therapeutically effective amount of at least one of any of the compounds herein, or pharmaceutically acceptable salt, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate.

In some embodiments, provided herein is the use of a compound disclosed herein for inhibiting Menin-MLL activity or for the treatment of a disease, disorder, or condition, which would benefit from inhibition of Menin-MLL activity.

In some embodiments, compounds provided herein are administered to a human.

In some embodiments, compounds provided herein are orally administered.

In some embodiments, compounds provided herein are used for the formulation of a medicament for the inhibition of Menin-MLL activity. In some embodiments, compounds provided herein are used for the formulation of a medicament for the inhibition of Menin-MLL activity.

Articles of manufacture including packaging material, a compound or composition or pharmaceutically acceptable derivative thereof provided herein, which is effective for inhibiting the activity of Menin-MLL, within the packaging material, and a label that indicates that the compound or composition, or pharmaceutically acceptable salt, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate thereof, is used for inhibiting the activity of Menin-MLL, are provided.

In some embodiments, provided herein is a method for inhibiting Menin-MLL activity in a subject in need thereof by administering to the subject thereof a composition containing a therapeutically effective amount of at least one compound having the structure of Formula (I). In some embodiments, the subject in need is suffering from an autoimmune disease, e.g., inflammatory bowel disease, arthritis, lupus, rheumatoid arthritis, psoriatic arthritis, osteoarthritis, Still's disease, juvenile arthritis, diabetes, myasthenia gravis, Hashimoto's thyroiditis, Ord's thyroiditis, Graves' disease Sjögren's syndrome, multiple sclerosis, Guillain-Barré syndrome, acute disseminated encephalomyelitis, Addison's disease, opsoclonus-myoclonus syndrome, ankylosing spondylitis, antiphospholipid antibody syndrome, aplastic anemia, autoimmune hepatitis, coeliac disease, Goodpasture's syndrome, idiopathic thrombocytopenic purpura, optic neuritis, scleroderma, primary biliary cirrhosis, Reiter's syndrome, Takayasu's arteritis, temporal arteritis, warm autoimmune hemolytic anemia, Wegener's granulomatosis, psoriasis, alopecia universalis, Beliefs disease, chronic fatigue, dysautonomia, endometriosis, interstitial cystitis, neuromyotonia, scleroderma, or vulvodynia.

In some embodiments, the subject in need is suffering from a heteroimmune condition or disease, e.g., graft versus host disease, transplantation, transfusion, anaphylaxis, allergy, type I hypersensitivity, allergic conjunctivitis, allergic rhinitis, or atopic dermatitis.

In certain embodiments, the subject in need is suffering from an inflammatory disease, e.g., asthma, appendicitis, blepharitis, bronchiolitis, bronchitis, bursitis, cervicitis, cholangitis, cholecystitis, colitis, conjunctivitis, cystitis, dacryoadenitis, dermatitis, dermatomyositis, encephalitis, endocarditis, endometritis, enteritis, enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis, gastritis, gastroenteritis, hepatitis, hidradenitis suppurativa, laryngitis, mastitis, meningitis, myelitis myocarditis, myositis, nephritis, oophoritis, orchitis, osteitis, otitis, pancreatitis, parotitis, pericarditis, peritonitis, pharyngitis, pleuritis, phlebitis, pneumonitis, pneumonia, proctitis, prostatitis, pyelonephritis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis, tendonitis, tonsillitis, uveitis, vaginitis, vasculitis, or vulvitis.

In some embodiments, the subject in need is suffering from a cancer. In some embodiments, the cancer is a B-cell proliferative disorder, e.g., diffuse large B cell lymphoma, follicular lymphoma, chronic lymphocytic lymphoma, chronic lymphocytic leukemia, B-cell prolymphocytic leukemia, lymphoplasmacytic lymphoma/Waldenström macroglobulinemia, splenic marginal zone lymphoma, plasma cell myeloma, plasmacytoma, extranodal marginal zone B cell lymphoma, nodal marginal zone B cell lymphoma, mantle cell lymphoma, mediastinal (thymic) large B cell lymphoma, intravascular large B cell lymphoma, primary effusion lymphoma, burkitt lymphoma/leukemia, or lymphomatoid granulomatosis. In some embodiments, where the subject is suffering from a cancer, an anti-cancer agent is administered to the subject in addition to one of the above-mentioned compounds.

In some embodiments, the subject in need is suffering from a thromboembolic disorder, e.g., myocardial infarct, angina pectoris, reocclusion after angioplasty, restenosis after angioplasty, reocclusion after aortocoronary bypass, restenosis after aortocoronary bypass, stroke, transitory ischemia, a peripheral arterial occlusive disorder, pulmonary embolism, or deep venous thrombosis.

In some embodiments, provided herein is a method for treating an autoimmune disease by administering to a subject in need thereof a composition containing a therapeutically effective amount of at least one compound having the structure of Formula (I)-(XXIIIh). In some embodiments, the autoimmune disease is arthritis. In some embodiments, the autoimmune disease is lupus. In some embodiments, the autoimmune disease is inflammatory bowel disease (including Crohn's disease and ulcerative colitis), rheumatoid arthritis, psoriatic arthritis, osteoarthritis, Still's disease, juvenile arthritis, lupus, diabetes, myasthenia gravis, Hashimoto's thyroiditis, Ord's thyroiditis, Graves' disease Sjögren's syndrome, multiple sclerosis, Guillain-Barré syndrome, acute disseminated encephalomyelitis, Addison's disease, opsoclonus-myoclonus syndrome, ankylosing spondylitis, antiphospholipid antibody syndrome, aplastic anemia, autoimmune hepatitis, coeliac disease, Goodpasture's syndrome, idiopathic thrombocytopenic purpura, optic neuritis, scleroderma, primary biliary cirrhosis, Reiter's syndrome, Takayasu's arteritis, temporal arteritis, warm autoimmune hemolytic anemia, Wegener's granulomatosis, psoriasis, alopecia universalis, Behçet's disease, chronic fatigue, dysautonomia, endometriosis, interstitial cystitis, neuromyotonia, scleroderma, or vulvodynia.

In some embodiments, provided herein is a method for treating a heteroimmune condition or disease by administering to a subject in need thereof a composition containing a therapeutically effective amount of at least one compound having the structure Formula (I)-(XXIIIh). In some embodiments, the heteroimmune condition or disease is graft versus host disease, transplantation, transfusion, anaphylaxis, allergy, type I hypersensitivity, allergic conjunctivitis, allergic rhinitis, or atopic dermatitis.

In some embodiments, provided herein is a method for treating an inflammatory disease by administering to a subject in need thereof a composition containing a therapeutically effective amount of at least one compound having the structure of Formula (I)-(XXIIIh). In some embodiments, the inflammatory disease is asthma, inflammatory bowel disease (including Crohn's disease and ulcerative colitis), appendicitis, blepharitis, bronchiolitis, bronchitis, bursitis, cervicitis, cholangitis, cholecystitis, colitis, conjunctivitis, cystitis, dacryoadenitis, dermatitis, dermatomyositis, encephalitis, endocarditis, endometritis, enteritis, enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis, gastritis, gastroenteritis, hepatitis, hidradenitis suppurativa, laryngitis, mastitis, meningitis, myelitis myocarditis, myositis, nephritis, oophoritis, orchitis, osteitis, otitis, pancreatitis, parotitis, pericarditis, peritonitis, pharyngitis, pleuritis, phlebitis, pneumonitis, pneumonia, proctitis, prostatitis, pyelonephritis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis, tendonitis, tonsillitis, uveitis, vaginitis, vasculitis, or vulvitis.

In some embodiments, provided herein is a method for treating a cancer by administering to a subject in need thereof a composition containing a therapeutically effective amount of at least one compound having the structure of Formula (I)-(XXIIIh). In some embodiments, the cancer is a B-cell proliferative disorder, e.g., diffuse large B cell lymphoma, follicular lymphoma, chronic lymphocytic lymphoma, chronic lymphocytic leukemia, B-cell prolymphocytic leukemia, lymphoplasmacytic lymphoma/Waldenström macroglobulinemia, splenic marginal zone lymphoma, plasma cell myeloma, plasmacytoma, extranodal marginal zone B cell lymphoma, nodal marginal zone B cell lymphoma, mantle cell lymphoma, mediastinal (thymic) large B cell lymphoma, intravascular large B cell lymphoma, primary effusion lymphoma, burkitt lymphoma/leukemia, or lymphomatoid granulomatosis. In some embodiments, where the subject is suffering from a cancer, an anti-cancer agent is administered to the subject in addition to one of the above-mentioned compounds.

In some embodiments, provided herein is a method for treating a thromboembolic disorder by administering to a subject in need thereof a composition containing a therapeutically effective amount of at least one compound having the structure of Formula (I)-(XXIIIh). In some embodiments, the thromboembolic disorder is myocardial infarct, angina pectoris, reocclusion after angioplasty, restenosis after angioplasty, reocclusion after aortocoronary bypass, restenosis after aortocoronary bypass, stroke, transitory ischemia, a peripheral arterial occlusive disorder, pulmonary embolism, or deep venous thrombosis.

In some embodiments are methods for treating inflammation comprising administering to the mammal at least once an effective amount of at least one compound having the structure of Formula (I)-(XXIIIh).

In some embodiments, the present invention provides methods for the treatment of cancer comprising administering to the mammal at least once an effective amount of at least one compound having the structure of Formula (I)-(XXIIIh). The type of cancer may include, but is not limited to, pancreatic cancer and other solid or hematological tumors.

In some embodiments, the present invention provides methods for treating respiratory diseases comprising administering to the mammal at least once an effective amount of at least one compound having the structure Formula (I)-(XXIIIh). In a some embodiments, the respiratory disease is asthma. In some embodiments, the respiratory disease includes, but is not limited to, adult respiratory distress syndrome and allergic (extrinsic) asthma, non-allergic (intrinsic) asthma, acute severe asthma, chronic asthma, clinical asthma, nocturnal asthma, allergen-induced asthma, aspirin-sensitive asthma, exercise-induced asthma, isocapnic hyperventilation, child-onset asthma, adult-onset asthma, cough-variant asthma, occupational asthma, steroid-resistant asthma, and seasonal asthma.

In some embodiments, the present invention provides methods for preventing rheumatoid arthritis and osteoarthritis comprising administering to the mammal at least once an effective amount of at least one compound having the structure of Formula (I)-(XXIIIh).

In some embodiments, the present invention provides methods for treating inflammatory responses of the skin comprising administering to the mammal at least once an effective amount of at least one compound having the structure of Formula (I)-(XXIIIh). Such inflammatory responses of the skin include, by way of example, dermatitis, contact dermatitis, eczema, urticaria, rosacea, and scarring. In another aspect are methods for reducing psoriatic lesions in the skin, joints, or other tissues or organs, comprising administering to the mammal an effective amount of a first compound having the structure of Formula (I)-(XXIIIh)

In certain embodiments, the present invention discloses methods for treating the following diseases or conditions comprising administering to the mammal a compound of the invention. In some embodiments, the disease or condition is ALL (Acute Lymphoblastic Lymphoma), DLBCL (Diffuse Large B-Cell Lymphoma), FL (Follicular Lymphoma), RCC (Renal Cell Carcinoma), Childhoon Medulloblastoma, Glioblastoma, Pancreatic tumor or cancer, Liver cancer (Hepatocellular Carcinoma), Prostate Cancer (Myc), Triple Negative Breast (Myc), AML (Acute Myeloid Leukemia), or MDS (Myelo Dyslplastic Syndrome). In some embodiments, the disease or condition is Early-onset Dystonia. In yet some embodiments, the disease or condition is Kabuki Syndrome.

In some embodiments, the disease or condition is p53 driven tumor.

p53 Driven Tumors and Menin/MLL1

RUNX2 signaling pathway is one of survival signals specific to p53 defective cancer cells. RUNX2 recruits the Menin/MLL1 epigenetic complex to induce the expression of MYC. Using small molecule inhibitors of the Menin/MLL1 complex, targeting RUNX2/Menin/MLL1/MYC axis is a feasible strategy for killing p53 defective cancer cells (Shih, et al., A RUNX2-Mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells. PLOS Genetics, https://doi.org/10.1371/journal.pgen.1005884, 2016).

In some embodiments, the disease or condition is MYC driven tumor.

MYC Driven Tumors and Menin/MLL1

MYC is documented to be involved broadly in many cancers, in which its expression is estimated to be elevated or deregulated in up to 70% of human cancers. High levels of MYC expression have been linked to aggressive human prostate cancer and triple negative breast cancer (Gurel et al., Mod Pathol. 2008 September; 21(9): 1156-67; Palaskas et al., Cancer Res. 2011 Aug. 1; 71(15); 5164-74). Experimental models of Myc-mediated tumorigenesis suggest that established tumors are addicted to Myc and that deregulated expression of Myc result in an addiction not only to Myc but also to nutrients. These Myc-induced changes provide a unique opportunity for new therapeutic strategies. Notwithstanding the fact that normal proliferating cells (stem cell compartments and immune cells) also use MYC for renewal, many studies have focused on targeting Myc for cancer therapeutics. Strategies have emerged to inhibit MYC expression, to interrupt Myc-Max dimerization, to inhibit Myc-Max DNA binding, and to interfere with key Myc target genes (Dang et al. Cell. 2012, 149(1): 22-35).

Menin's role in tumor suppression is cell-specific, Menin disruption in the liver or haematopoietic system does not result in tumors. Important to measure the concentration of the drug in endocrine tissue, liver tissue, bone marrow, and Haematopoietic.

In any of the aforementioned embodiments are some embodiments in which administration is enteral, parenteral, or both, and wherein (a) an effective amount of a provided compound is systemically administered to the mammal; (b) an effective amount of a provided compound is administered orally to the mammal; (c) an effective amount of a provided compound is intravenously administered to the mammal; (d) an effective amount of a provided compound is administered by inhalation; (e) an effective amount of a provided compound is administered by nasal administration; or (f) an effective amount of a provided compound is administered by injection to the mammal; (g) an effective amount of a provided compound is administered topically (dermal) to the mammal; (h) an effective amount of a provided compound is administered by ophthalmic administration; or (i) an effective amount of a provided compound is administered rectally to the mammal.

In any of the aforementioned embodiments are some embodiments comprising single administrations of an effective amount of a provided compound is, including some embodiments in which (i) a provided compound is administered once; (ii) a provided compound is administered to the mammal multiple times over the span of one day; (iii) continually; or (iv) continuously.

In any of the aforementioned embodiments are some embodiments comprising multiple administrations of an effective amount of a provided compound, including some embodiments in which (i) a provided compound is administered in a single dose; (ii) the time between multiple administrations is every 6 hours; (iii) a provided compound is administered to the mammal every 8 hours. In some embodiments, the method comprises a drug holiday, wherein the administration of the compound is temporarily suspended or the dose of the compound being administered is temporarily reduced; at the end of the drug holiday, dosing of the compound is resumed. The length of the drug holiday can vary from 2 days to 1 year.

In any of the aforementioned embodiments involving the treatment of proliferative disorders, including cancer, are some embodiments comprising administering at least one additional agent selected from the group consisting of alemtuzumab, arsenic trioxide, asparaginase (pegylated or non-), bevacizumab, cetuximab, platinum-based compounds such as cisplatin, cladribine, daunorubicin/doxorubicin/idarubicin, irinotecan, fludarabine, 5-fluorouracil, gemtuzumab, methotrexate, Paclitaxel™, taxol, temozolomide, thioguanine, or classes of drugs including hormones (an antiestrogen, an antiandrogen, or gonadotropin releasing hormone analogues, interferons such as alpha interferon, nitrogen mustards such as busulfan or melphalan or mechlorethamine, retinoids such as tretinoin, topoisomerase inhibitors such as irinotecan or topotecan, tyrosine kinase inhibitors such as gefmitinib or imatinib, or agents to treat signs or symptoms induced by such therapy including allopurinol, filgrastim, granisetron/ondansetron/palonosetron, dronabinol.

In some embodiments, the compounds of Formula (I)-(XXIIIh) are inhibitors of Menin-MLL activity. In certain embodiments, such inhibitors have an IC₅₀ below 10 μM in enzyme assay. In some embodiments, a menin-MLL inhibitor has an IC₅₀ of less than 1 μM, and in some embodiments, less than 0.25 μM.

Other objects, features and advantages of the methods and compositions described herein will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments, are given by way of illustration only, since various changes and modifications within the spirit and scope of the present disclosure will become apparent to those skilled in the art from this detailed description. The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in the application including, but not limited to, patents, patent applications, articles, books, manuals, and treatises are hereby expressly incorporated by reference in their entirety for any purpose.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 shows comparison of MOLM13 IC₅₀ (day 7) of Compound 2 with MI-503.

FIG. 2 shows comparison of MOLM13 IC₅₀ (day 10) of Compound 2 with MI-503.

FIG. 3 shows comparison of THP1 IC₅₀ (day 3) of Compound 2 with MI-503.

FIG. 4 shows comparison of HL60 IC₅₀ (day 7) of Compound 2 with MI-503.

FIG. 5 shows effect of increasing concentrations of Compound 10, Compound 11, Compound 12, Compound 13 and MI-503 (0.027 μM-20 μM) on HL-60 cell proliferation after 4 days treatment, as detected by the CellTiterGlo Cell viability assay. Each data point is the mean±SEM of data from the individual experiment performed in duplicate.

FIG. 6 shows effect of increasing concentrations of Compound 10, Compound 11, Compound 12, Compound 13 and MI-503 (0.027 μM-20 μM) on MV-4-11 cell proliferation after 4 days treatment as detected by the CellTiterGlo Cell viability assay. Each data point is the mean±SEM of data from the individual experiment performed in duplicate.

FIG. 7 shows effect of increasing concentrations of Compound 10, Compound 11, Compound 12, Compound 13 and MI-503 (0.027 μM-20 μM) on MOLM-13 cell proliferation after 4 days treatment as detected by the CellTiterGlo Cell viability assay. Each data point is the mean±SEM of data from the individual experiment performed in duplicate.

FIG. 8 shows Long Term Proliferation Assay results of Compound 11, Compound 12, and MI-503.

DETAILED DESCRIPTION OF THE INVENTION

Certain Terminology

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the claimed subject matter belongs. In the event that there are a plurality of definitions for terms herein, those in this section prevail. Where reference is made to a URL or other such identifier or address, it is understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.

It is to be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of any subject matter claimed. In this application, the use of the singular includes the plural unless specifically stated otherwise. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Use of the term “including” as well as other forms, such as “include”, “includes,” and “included,” is not limiting. Pefinition of standard chemistry terms may be found in reference works, including Carey and Sundberg “ADVANCED ORGANIC CHEMISTRY 4^(TH) ED.” Vols. A (2000) and B (2001), Plenum Press, New York. Unless otherwise indicated, conventional methods of mass spectroscopy, NMR, HPLC, protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art are employed. Unless specific definitions are provided, the nomenclature employed in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those known in the art. Standard techniques can be used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients. Standard techniques can be used for recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation (e.g., electroporation, lipofection). Reactions and purification techniques can be performed e.g., using kits of manufacturer's specifications or as commonly accomplished in the art or as described herein. The foregoing techniques and procedures can be generally performed of conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification.

It is to be understood that the methods and compositions described herein are not limited to the particular methodology, protocols, cell lines, constructs, and reagents described herein and as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the methods and compositions described herein, which will be limited only by the appended claims.

All publications and patents mentioned herein are incorporated herein by reference in their entirety for the purpose of describing and disclosing, for example, the constructs and methodologies that are described in the publications, which might be used in connection with the methods, compositions and compounds described herein. The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the inventors described herein are not entitled to antedate such disclosure by virtue of prior invention or for any other reason.

“Alkyl” refers to a straight or branched hydrocarbon chain radical consisting solely of carbon and hydrogen atoms, containing no unsaturation, having from one to fifteen carbon atoms (e.g., C₁-C₁₅ alkyl). In certain embodiments, an alkyl comprises one to thirteen carbon atoms (e.g., C₁-C₁₃ alkyl). In certain embodiments, an alkyl comprises one to eight carbon atoms (e.g., C₁-C₈ alkyl). In some embodiments, an alkyl comprises five to fifteen carbon atoms (e.g., C₅-C₁₅ alkyl). In certain embodiments, an alkyl comprises five to eight carbon atoms (e.g., C₅-C_(x) alkyl). The alkyl is attached to the rest of the molecule by a single bond, for example, methyl (Me), ethyl (Et), n-propyl (n-pr), 1-methylethyl (iso-propyl or i-Pr), n-butyl (n-Bu), n-pentyl, 1,1-dimethylethyl (t-butyl, or t-Bu), 3-methylhexyl, 2-methylhexyl, and the like. Unless stated otherwise specifically in the specification, an alkyl group is optionally substituted as defined and described below and herein.

The alkyl group could also be a “lower alkyl” having 1 to 6 carbon atoms.

As used herein, C₁-C_(x) includes C₁-C₂, C₁-C₃ . . . C₁-C_(x).

“Alkenyl” refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one double bond, and having from two to twelve carbon atoms. In certain embodiments, an alkenyl comprises two to eight carbon atoms. In some embodiments, an alkenyl comprises two to four carbon atoms. The alkenyl is attached to the rest of the molecule by a single bond, for example, ethenyl (i.e., vinyl), prop-1-enyl (i.e., allyl), but-1-enyl, pent-1-enyl, penta-1,4-dienyl, and the like. Unless stated otherwise specifically in the specification, an alkenyl group is optionally substituted as defined and described below and herein.

“Alkynyl” refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one triple bond, having from two to twelve carbon atoms. In certain embodiments, an alkynyl comprises two to eight carbon atoms. In some embodiments, an alkynyl has two to four carbon atoms. The alkynyl is attached to the rest of the molecule by a single bond, for example, ethynyl, propynyl, butynyl, pentynyl, hexynyl, and the like. Unless stated otherwise specifically in the specification, an alkynyl group is optionally substituted as defined and described below and herein.

“Alkylene” or “alkylene chain” refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing no unsaturation and having from one to twelve carbon atoms, for example, methylene, ethylene, propylene, n-butylene, and the like. The alkylene chain is attached to the rest of the molecule through a single bond and to the radical group through a single bond. The points of attachment of the alkylene chain to the rest of the molecule and to the radical group can be through one carbon in the alkylene chain or through any two carbons within the chain. Unless stated otherwise specifically in the specification, an alkylene chain is optionally substituted as defined and described below and herein.

“Alkenylene” or “alkenylene chain” refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing at least one double bond and having from two to twelve carbon atoms, for example, ethenylene, propenylene, n-butenylene, and the like. The alkenylene chain is attached to the rest of the molecule through a double bond or a single bond and to the radical group through a double bond or a single bond. The points of attachment of the alkenylene chain to the rest of the molecule and to the radical group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, an alkenylene chain is optionally substituted as defined and described below and herein. “Aryl” refers to a radical derived from an aromatic monocyclic or multicyclic hydrocarbon ring system by removing a hydrogen atom from a ring carbon atom. The aromatic monocyclic or multicyclic hydrocarbon ring system contains only hydrogen and carbon from six to eighteen carbon atoms, where at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) π-electron system in accordance with the Hückel theory. Aryl groups include, but are not limited to, groups such as phenyl (Ph), fluorenyl, and naphthyl. Unless stated otherwise specifically in the specification, the term “aryl” or the prefix “ar-” (such as in “aralkyl”) is meant to include aryl radicals optionally substituted as defined and described below and herein.

“Aralkyl” refers to a radical of the formula —R^(c)-aryl where R^(c) is an alkyl ene chain as defined above, for example, benzyl, diphenylmethyl and the like. The alkylene chain part of the aralkyl radical is optionally substituted as described above for an alkylene chain. The aryl part of the aralkyl radical is optionally substituted as described above for an aryl group.

“Aralkenyl” refers to a radical of the formula —R^(d)-aryl where R^(d) is an alkenylene chain as defined above. The aryl part of the aralkenyl radical is optionally substituted as described above for an aryl group. The alkenylene chain part of the aralkenyl radical is optionally substituted as defined above for an alkenylene group.

“Aralkynyl” refers to a radical of the formula —R^(e)-aryl, where R^(e) is an alkynylene chain as defined above. The aryl part of the aralkynyl radical is optionally substituted as described above for an aryl group. The alkynylene chain part of the aralkynyl radical is optionally substituted as defined above for an alkynylene chain.

“Carbocyclyl” refers to a stable non-aromatic monocyclic or polycyclic hydrocarbon radical consisting solely of carbon and hydrogen atoms, which includes fused or bridged ring systems, having from three to fifteen carbon atoms. In certain embodiments, a carbocyclyl comprises three to ten carbon atoms. In some embodiments, a carbocyclyl comprises five to seven carbon atoms. The carbocyclyl is attached to the rest of the molecule by a single bond. Carbocyclyl is optionally saturated, (i.e., containing single C—C bonds only) or unsaturated (i.e., containing one or more double bonds or triple bonds.) A fully saturated carbocyclyl radical is also referred to as “cycloalkyl.” Examples of monocyclic cycloalkyls include, e.g., cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. An unsaturated carbocyclyl is also referred to as “cycloalkenyl.” Examples of monocyclic cycloalkenyls include, e.g., cyclopentenyl, cyclohexenyl, cycloheptenyl, and cyclooctenyl. Polycyclic carbocyclyl radicals include, for example, adamantyl, norbornyl (i.e., bicyclo[2.2.1]heptanyl), norbornenyl, decalinyl, 7,7-dimethyl-bicyclo[2.2.1]heptanyl, and the like. Unless otherwise stated specifically in the specification, the term “carbocyclyl” is meant to include carbocyclyl radicals that are optionally substituted as defined and described below and herein. “Halo” or “halogen” refers to bromo, chloro, fluoro or iodo substituents.

The terms “haloalkyl,” “haloalkenyl,” “haloalkynyl” and “haloalkoxy” include alkyl, alkenyl, alkynyl and alkoxy structures in which at least one hydrogen is replaced with a halogen atom. In certain embodiments in which two or more hydrogen atoms are replaced with halogen atoms, the halogen atoms are all the same as one another. In some embodiments in which two or more hydrogen atoms are replaced with halogen atoms, the halogen atoms are not all the same as one another.

“Fluoroalkyl” refers to an alkyl radical, as defined above, that is substituted by one or more fluoro radicals, as defined above, for example, trifluoromethyl, difluoromethyl, 2,2,2-trifluoroethyl, 1-fluoromethyl-2-fluoroethyl, and the like. The alkyl part of the fluoroalkyl radical is optionally substituted as defined above for an alkyl group.

As used herein, the term “non-aromatic heterocycle”, “heterocycloalkyl” or “heteroalicyclic” refers to a non-aromatic ring wherein one or more atoms forming the ring is a heteroatom. A “non-aromatic heterocycle” or “heterocycloalkyl” group refers to a cycloalkyl group that includes at least one heteroatom selected from nitrogen, oxygen and sulfur. The radicals may be fused with an aryl or heteroaryl. Heterocycloalkyl rings can be formed by three to 14 ring atoms, such as three, four, five, six, seven, eight, nine, or more than nine atoms. Heterocycloalkyl rings can be optionally substituted. In certain embodiments, non-aromatic heterocycles contain one or more carbonyl or thiocarbonyl groups such as, for example, oxo- and thio-containing groups. Examples of heterocycloalkyls include, but are not limited to, lactams, lactones, cyclic imides, cyclic thioimides, cyclic carbamates, tetrahydrothiopyran, 4H-pyran, tetrahydropyran, piperidine, 1,3-dioxin, 1,3-dioxane, 1,4-dioxin, 1,4-dioxane, piperazine, 1,3-oxathiane, 1,4-oxathiin, 1,4-oxathiane, tetrahydro-1,4-thiazine, 2H-1,2-oxazine, maleimide, succinimide, barbituric acid, thiobarbituric acid, dioxopiperazine, hydantoin, dihydrouracil, morpholine, trioxane, hexahydro-1,3,5-triazine, tetrahydrothiophene, tetrahydrofuran, pyrroline, pyrrolidine, pyrrolidone, pyrrolidione, pyrazoline, pyrazolidine, imidazoline, imidazolidine, 1,3-dioxole, 1,3-dioxolane, 1,3-dithiole, 1,3-dithiolane, isoxazoline, isoxazolidine, oxazoline, oxazolidine, oxazolidinone, thiazoline, thiazolidine, and 1,3-oxathiolane. Illustrative examples of heterocycloalkyl groups, also referred to as non-aromatic heterocycles, include:

and the like. The term heteroalicyclic also includes all ring forms of the carbohydrates, including but not limited to the monosaccharides, the disaccharides and the oligosaccharides. Depending on the structure, a heterocycloalkyl group can be a monoradical or a diradical (i.e., a heterocycloalkylene group).

“Heteroaryl” refers to a radical derived from a 3- to 18-membered aromatic ring radical that comprises two to seventeen carbon atoms and from one to six heteroatoms selected from nitrogen, oxygen and sulfur. As used herein, the heteroaryl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, wherein at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) π-electron system in accordance with the Hückel theory. Heteroaryl includes fused or bridged ring systems. In some embodiments, heteroaryl rings have five, six, seven, eight, nine, or more than nine ring atoms. The heteroatom(s) in the heteroaryl radical is optionally oxidized. One or more nitrogen atoms, if present, are optionally quaternized. The heteroaryl is attached to the rest of the molecule through any atom of the ring(s). Examples of heteroaryls include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzindolyl, 1,3-benzodioxolyl, benzofuranyl, benzooxazolyl, benzo[d]thiazolyl, benzothiadiazolyl, benzo[b][1,4]dioxepinyl, benzo[b][1,4]oxazinyl, 1,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl), benzothieno[3,2-d]pyrimidinyl, benzotriazolyl, benzo[4,6]imidazo[1,2-a]pyridinyl, carbazolyl, cinnolinyl, cyclopenta[d]pyrimidinyl, 6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidinyl, 5,6-dihydrobenzo[h]quinazolinyl, 5,6-dihydrobenzo[h]cinnolinyl, 6,7-dihydro-5H-benzo[6,7]cyclohepta[1,2-c]pyridazinyl, dibenzofuranyl, dibenzothiophenyl, furanyl, furanonyl, furo[3,2-c]pyridinyl, 5,6,7,8,9,10-hexahydrocycloocta[d]pyrimidinyl, 5,6,7,8,9,10-hexahydrocycloocta[d]pyridazinyl, 5,6,7,8,9,10-hexahydrocycloocta[d]pyridinyl, isothiazolyl, imidazolyl, indazolyl, indolyl, indazolyl, isoindolyl, indolinyl, isoindolinyl, isoquinolyl, indolizinyl, isoxazolyl, 5,8-methano-5,6,7,8-tetrahydroquinazolinyl, naphthyridinyl, 1,6-naphthyridinonyl, oxadiazolyl, 2-oxoazepinyl, oxazolyl, oxiranyl, 5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazolinyl, 1-phenyl-1H-pyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl, pteridinyl, purinyl, pyrrolyl, pyrazolyl, pyrazolo[3,4-d]pyrimidinyl, pyridinyl, pyrido[3,2-d]pyrimidinyl, pyrido[3,4-d]pyrimidinyl, pyrazinyl, pyrimidinyl, pyridazinyl, pyrrol yl, quinazolinyl, quinoxalinyl, quinolinyl, isoquinolinyl, tetrahydroquinolinyl, 5,6,7,8-tetrahydroquinazolinyl, 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidinyl, 6,7,8,9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidinyl, 5,6,7,8-tetrahydropyrido[4,5-c]pyridazinyl, thiazolyl, thiadiazolyl, triazolyl, tetrazolyl, triazinyl, thieno[2,3-d]pyrimidinyl, thieno[3,2-d]pyrimidinyl, thieno[2,3-c]pyridinyl, and thiophenyl (i.e. thienyl). Unless stated otherwise specifically in the specification, the term “heteroaryl” is meant to include heteroaryl radicals as defined above which are optionally substituted as defined and described below and herein.

“A-heteroaryl” refers to a heteroaryl radical as defined above containing at least one nitrogen and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a nitrogen atom in the heteroaryl radical. An A-heteroaryl radical is optionally substituted as described above for heteroaryl radicals.

“C-heteroaryl” refers to a heteroaryl radical as defined above and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a carbon atom in the heteroaryl radical. A C-heteroaryl radical is optionally substituted as described above for heteroaryl radicals.

“Heteroarylalkyl” refers to a radical of the formula —R^(c)-heteroaryl, where R^(c) is an alkylene chain as defined above. If the heteroaryl is a nitrogen-containing heteroaryl, the heteroaryl is optionally attached to the alkyl radical at the nitrogen atom. The alkylene chain of the heteroarylalkyl radical is optionally substituted as defined above for an alkylene chain. The heteroaryl part of the heteroarylalkyl radical is optionally substituted as defined above for a heteroaryl group.

“Sulfanyl” refers to the —S— radical.

“Sulfinyl” refers to the —S(═O)— radical.

“Sulfonyl” refers to the —S(═O)₂— radical.

“Amino” refers to the —NH₂ radical.

“Cyano” refers to the —CN radical.

“Nitro” refers to the —NO₂ radical.

“Oxa” refers to the —O— radical.

“Oxo” refers to the ═O radical.

“Imino” refers to the ═NH radical.

“Thioxo” refers to the ═S radical.

An “alkoxy” group refers to a (alkyl)O— group, where alkyl is as defined herein.

An “aryloxy” group refers to an (aryl)O— group, where aryl is as defined herein.

“Carbocyclylalkyl” means an alkyl radical, as defined herein, substituted with a carbocyclyl group. “Cycloalkylalkyl” means an alkyl radical, as defined herein, substituted with a cycloalkyl group. Non-limiting cycloalkylalkyl groups include cyclopropylmethyl, cyclobutylmethyl, cyclopentylmethyl, cyclohexylmethyl, and the like.

As used herein, the terms “heteroalkyl” “heteroalkenyl” and “heteroalkynyl” include optionally substituted alkyl, alkenyl and alkynyl radicals in which one or more skeletal chain atoms is a heteroatom, e.g., oxygen, nitrogen, sulfur, silicon, phosphorus or combinations thereof. The heteroatom(s) may be placed at any interior position of the heteroalkyl group or at the position at which the heteroalkyl group is attached to the remainder of the molecule. Examples include, but are not limited to, —CH₂—O—CH₃, —CH₂—CH₂—O—CH₃, —CH₂—NH—CH₃, —CH₂—CH₂—NH—CH₃, —CH₂—N(CH₃)—CH₃, —CH₂—CH₂—NH—CH₃, —CH₂—CH₂—N(CH₃)—CH₃, —CH₂—S—CH₂—CH₃, —CH₂—CH₂, —S(O)—CH₃, —CH₂—CH₂—S(O)₂—CH₃, —CH═CH—O—CH₃, —Si(CH₃)₃, —CH₂—CH═N-OCH₃, and —CH═CH—N(CH₃)—CH₃, In addition, up to two heteroatoms may be consecutive, such as, by way of example, —CH₂—NH—OCH₃ and —CH₂—O—Si(CH₃)₃.

The term “heteroatom” refers to an atom other than carbon or hydrogen. Heteroatoms are typically independently selected from among oxygen, sulfur, nitrogen, silicon and phosphorus, but are not limited to these atoms. In embodiments in which two or more heteroatoms are present, the two or more heteroatoms can all be the same as one another, or some or all of the two or more heteroatoms can each be different from the others.

The term “bond,” “direct bond” or “single bond” refers to a chemical bond between two atoms, or two moieties when the atoms joined by the bond are considered to be part of larger substructure.

An “isocyanato” group refers to a —NCO group.

An “isothiocyanato” group refers to a —NCS group.

The term “moiety” refers to a specific segment or functional group of a molecule. Chemical moieties are often recognized chemical entities embedded in or appended to a molecule.

A “thioalkoxy” or “alkylthio” group refers to a —S-alkyl group.

A “alkylthioalkyl” group refers to an alkyl group substituted with a —S-alkyl group.

As used herein, the term “acyloxy” refers to a group of formula RC(═O)O—.

“Carboxy” means a —C(O)OH radical.

As used herein, the term “acetyl” refers to a group of formula —C(═O)CH₃.

“Acyl” refers to the group —C(O)R.

As used herein, the term “trihalomethanesulfonyl” refers to a group of formula X₃CS(═O)₂— where X is a halogen.

“Cyanoalkyl” means an alkyl radical, as defined herein, substituted with at least one cyano group.

As used herein, the term “N-sulfonamido” or “sulfonylamino” refers to a group of formula RS(═O)₂NH—.

As used herein, the term “O-carbamyl” refers to a group of formula —OC(═O)NR₂.

As used herein, the term “N-carbamyl” refers to a group of formula ROC(═O)NH—.

As used herein, the term “O-thiocarbamyl” refers to a group of formula —OC(═S)NR₂.

As used herein, “N-thiocarbamyl” refers to a group of formula ROC(═S)NH—.

As used herein, the term “C-amido” refers to a group of formula —C(═O)NR₂.

“Aminocarbonyl” refers to a —CONH₂ radical.

As used herein, the term “N-amido” refers to a group of formula RC(═O)NH—.

“Hydroxyalkyl” refers to an alkyl radical, as defined herein, substituted with at least one hydroxy group. Non-limiting examples of a hydroxyalkyl include, but are not limited to, hydroxymethyl, 2-hydroxyethyl, 2-hydroxypropyl, 3-hydroxypropyl, 1-(hydroxymethyl)-2-methylpropyl, 2-hydroxybutyl, 3-hydroxybutyl, 4-hydroxybutyl, 2,3-dihydroxypropyl, 1-(hydroxymethyl)-2-hydroxyethyl, 2,3-dihydroxybutyl, 3,4-dihydroxybutyl and 2-(hydroxymethyl)-3-hydroxypropyl.

“Alkoxyalkyl” refers to an alkyl radical, as defined herein, substituted with an alkoxy group, as defined herein.

An “alkenyloxy” group refers to a (alkenyl)O— group, where alkenyl is as defined herein.

The term “alkylamine” refers to the —N(alkyl)_(x)H_(y) group, where x and y are selected from among x=1, y=1 and x=2, y=0. When x=2, the alkyl groups, taken together with the N atom to which they are attached, can optionally form a cyclic ring system.

“Alkylaminoalkyl” refers to an alkyl radical, as defined herein, substituted with an alkylamine, as defined herein.

An “amide” is a chemical moiety with the formula —C(O)NHR or —NHC(O)R, where R is selected from among alkyl, cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) and heteroalicyclic (bonded through a ring carbon). An amide moiety may form a linkage between an amino acid or a peptide molecule and a compound described herein, thereby forming a prodrug. Any amine, or carboxyl side chain on the compounds described herein can be amidified. The procedures and specific groups to make such amides are known to those of skill in the art and can readily be found in reference sources such as Greene and Wuts, Protective Groups in Organic Synthesis, 3^(rd) Ed., John Wiley & Sons, New York, N.Y., 1999, which is incorporated herein by reference in its entirety.

The term “ester” refers to a chemical moiety with formula —COOR, where R is selected from among alkyl, cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) and heteroalicyclic (bonded through a ring carbon). Any hydroxy, or carboxyl side chain on the compounds described herein can be esterified. The procedures and specific groups to make such esters are known to those of skill in the art and can readily be found in reference sources such as Greene and Wuts, Protective Groups in Organic Synthesis, 3^(rd) Ed., John Wiley & Sons, New York, N.Y., 1999, which is incorporated herein by reference in its entirety.

As used herein, the term “ring” refers to any covalently closed structure. Rings include, for example, carbocycles (e.g., aryls and cycloalkyls), heterocycles (e.g., heteroaryls and non-aromatic heterocycles), aromatics (e.g. aryls and heteroaryls), and non-aromatics (e.g., cycloalkyls and non-aromatic heterocycles). Rings can be optionally substituted. Rings can be monocyclic or polycyclic.

As used herein, the term “ring system” refers to one, or more than one ring.

The term “membered ring” can embrace any cyclic structure. The term “membered” is meant to denote the number of skeletal atoms that constitute the ring. Thus, for example, cyclohexyl, pyridine, pyran and thiopyran are 6-membered rings and cyclopentyl, pyrrole, furan, and thiophene are 5-membered rings.

The term “fused” refers to structures in which two or more rings share one or more bonds.

As described herein, compounds of the invention may be “optionally substituted”. In general, the term “substituted,” whether preceded by the term “optionally” or not, means that one or more hydrogens of a designated moiety are replaced with a suitable substituent. Unless otherwise indicated, an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds. The term “stable,” as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein.

Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; —(CH₂)₀₋₄R^(∘); —(CH₂)₀₋₄OR^(∘); —O(CH₂)₀₋₄R^(∘), —O—(CH₂)₀₋₄C(O)OR^(∘); —(CH₂)₀₋₄CH(OR^(∘))₂; —(CH₂)₀₋₄SR^(∘); —(CH₂)₀₋₄Ph, which may be substituted with R^(∘); —(CH₂)₀₋₄O(CH₂)₀₋₁Ph which may be substituted with R^(∘); —CH═CHPh, which may be substituted with R^(∘); —(CH₂)₀₋₄O(CH₂)₀₋₁-pyridyl which may be substituted with R^(∘); —NO₂; —CN; —N₃; —(CH₂)₀₋₄N(R^(∘))₂; —(CH₂)₀₋₄N(R^(∘))C(O)R^(∘); —N(R^(∘))C(S)R^(∘); —(CH₂)₀₋₄N(R^(∘))C(O)NR^(∘) ₂; —N(R^(∘))C(S)NR^(∘) ₂; —(CH₂)₀₋₄N(R^(∘))C(O)OR^(∘); —N(R^(∘))N(R^(∘))C(O)R^(∘); —N(R^(∘))N(R^(∘))C(O)NR^(∘) ₂; —N(R^(∘))N(R^(∘))C(O)OR^(∘); —(CH₂)₀₋₄C(O)R^(∘); —C(S)R^(∘); —(CH₂)₀₋₄C(O)OR^(∘); —(CH₂)₀₋₄C(O)SR^(∘); —(CH₂)₀₋₄C(O)OSiR^(∘) ₃; —(CH₂)₀₋₄C(O)R^(∘); —OC(O)(CH₂)₀₋₄SR—, —SC(S)SR^(∘); —(CH₂)₀₋₄SC(O)R^(∘); —(CH₂)₀₋₄C(O)NR^(∘) ₂; —C(S)NR^(∘) ₂; —C(S)SR^(∘); —(CH₂)₀₋₄OC(O)NR^(∘) ₂; —C(O)N(OR^(∘))R^(∘); —C(O)C(O)R^(∘); —C(O)CH₂C(O)R^(∘); —C(NOR^(∘))R^(∘); —(CH₂)₀₋₄SSR^(∘); —(CH₂)₀₋₄S(O)₂R^(∘); —(CH₂)₀₋₄S(O)₂OR^(∘); —(CH₂)₀₋₄S(O)₂R^(∘); —S(O)₂NR^(∘) ₂; —(CH₂)₀₋₄S(O)R^(∘); —N(R^(∘))S(O)₂NR^(∘) ₂; —N(R^(∘))S(O)₂R^(∘); —N(OR^(∘))R^(∘); —C(NH)NR^(∘) ₂; —P(O)₂R^(∘); —P(O)R^(∘) ₂; —OP(O)R^(∘) ₂; —OP(O)(OR^(∘))₂; SiR^(∘) ₃; —(C₁₋₄ straight or branched alkylene)O—N(R^(∘))₂; or —(C₁₋₄ straight or branched alkylene)C(O)O—N(R^(∘))₂, wherein each R^(∘) may be substituted as defined below and is independently hydrogen, C₁₋₆ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, —CH₂-(5-6 membered heteroaryl ring), or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R^(∘), taken together with their intervening atom(s), form a 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below.

Suitable monovalent substituents on R^(∘) (or the ring formed by taking two independent occurrences of R^(∘) together with their intervening atoms), are independently halogen, —(CH₂)₀₋₂R^(●), —(haloR^(●)), —(CH₂)₀₋₂OH, —(CH₂)₀₋₂OR^(●), —(CH₂)₀₋₂CH(OR^(●))₂; —O(haloR^(●)), —CN, —N₃, —(CH₂)₀₋₂C(O)R^(●), —(CH₂)₀₋₂C(O)OH, —(CH₂)₀₋₂C(O)OR^(●), —(CH₂)₀₋₂SR^(●) —(CH₂)₀₋₂SH, —(CH₂)₀₋₂NH₂, —(CH₂)₀₋₂NHR^(●), —(CH₂)₀₋₂NR^(●)2, —NO₂, —SiR^(●) ₃, —OSiR^(●) ₃, —C(O)SR^(●), —(C₁₋₄ straight or branched alkylene)C(O)OR^(●), or —SSR^(●) wherein each R^(●) is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently selected from C₁₋₄ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents on a saturated carbon atom of R^(∘) include ═O and ═S.

Suitable divalent substituents on a saturated carbon atom of an “optionally substituted” group include the following: ═O, ═S, ═NNR*₂, ═NNHC(O)R*, ═NNHC(O)OR*, ═NNHS(O)₂R*, ═NR*, ═NOR*, —O(C(R*₂))₂₋₃O—, or —S(C(R*₂))₂₋₃S—, wherein each independent occurrence of R* is selected from hydrogen, C₁₋₆ aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: —O(CR*₂)₂₋₃O—, wherein each independent occurrence of R* is selected from hydrogen, C₁₋₆ aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

Suitable substituents on the aliphatic group of R* include halogen, —R^(●), —(haloR^(●)), —OH, —OR^(●), —O(haloR^(●)), —CN, —C(O)OH, —C(O)OR^(●), —NH₂, —NHR^(●), —NR^(●) ₂, or —NO₂, wherein each R^(●) is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C₁₋₄ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include —R^(†), —NR^(†) ₂, —C(O)R^(†), —C(O)OR^(†), —C(O)C(O)R^(†), —C(O)CH₂C(O)R^(†), —S(O)₂R^(†), —S(O)₂NR^(†) ₂, —C(S)NR^(†) ₂, —C(NH)NR^(†) ₂, or —N(R^(†))S(O)₂R^(†); wherein each R^(†) is independently hydrogen, C₁₋₆ aliphatic which may be substituted as defined below, unsubstituted —OPh, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R^(†), taken together with their intervening atom(s) form an unsubstituted 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

Suitable substituents on the aliphatic group of R^(†) are independently halogen, —R^(●), —(haloR^(●)), —OH, —OR^(●), —O(haloR′), —CN, —C(O)OH, —C(O)OR^(●), —NH₂, —NHR^(●), —NR^(●) ₂, or —NO₂, wherein each R^(●) is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C₁₋₄ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

The term “nucleophile” or “nucleophilic” refers to an electron rich compound, or moiety thereof.

The term “electrophile”, or “electrophilic” refers to an electron poor or electron deficient molecule, or moiety thereof. Examples of electrophiles include, but in no way are limited to, Michael acceptor moieties.

The term “acceptable” or “pharmaceutically acceptable”, with respect to a formulation, composition or ingredient, as used herein, means having no persistent detrimental effect on the general health of the subject being treated or does not abrogate the biological activity or properties of the compound, and is relatively nontoxic.

As used herein, “amelioration” of the symptoms of a particular disease, disorder or condition by administration of a particular compound or pharmaceutical composition refers to any lessening of severity, delay in onset, slowing of progression, or shortening of duration, whether permanent or temporary, lasting or transient that can be attributed to or associated with administration of the compound or composition.

“Bioavailability” refers to the percentage of the weight of compounds disclosed herein, such as, compounds of any of Formula (I)-(XXIIIh) dosed that is delivered into the general circulation of the animal or human being studied. The total exposure (AUC_((0-∞))) of a drug when administered intravenously is usually defined as 100% bioavailable (F %). “Oral bioavailability” refers to the extent to which compounds disclosed herein, such as, compounds of any of Formula (I)-(XXIIIh) are absorbed into the general circulation when the pharmaceutical composition is taken orally as compared to intravenous injection.

“Blood plasma concentration” refers to the concentration of compounds disclosed herein, such as, compounds of any of Formula (I)-(XXIIIh) in the plasma component of blood of a subject. It is understood that the plasma concentration of compounds of any of Formula (I)-(XXIIIh) may vary significantly between subjects, due to variability with respect to metabolism and/or possible interactions with other therapeutic agents. In accordance with some embodiments disclosed herein, the blood plasma concentration of the compounds of any of Formula (I)-(XXIIIh) may vary from subject to subject. Likewise, values such as maximum plasma concentration (C_(max)) or time to reach maximum plasma concentration (T_(max)), or total area under the plasma concentration time curve (AUC_((0-∞))) may vary from subject to subject. Due to this variability, the amount necessary to constitute “a therapeutically effective amount” of a compound of any of Formula (I)-(XXIIIh) may vary from subject to subject.

The terms “co-administration” or the like, as used herein, are meant to encompass administration of the selected therapeutic agents to a single patient, and are intended to include treatment regimens in which the agents are administered by the same or different route of administration or at the same or different time.

The terms “effective amount” or “therapeutically effective amount,” as used herein, refer to a sufficient amount of an agent or a compound being administered which will relieve to some extent one or more of the symptoms of the disease or condition being treated. The result can be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. For example, an “effective amount” for therapeutic uses is the amount of the composition including a compound as disclosed herein required to provide a clinically significant decrease in disease symptoms without undue adverse side effects. An appropriate “effective amount” in any individual case may be determined using techniques, such as a dose escalation study. The term “therapeutically effective amount” includes, for example, a prophylactically effective amount. An “effective amount” of a compound disclosed herein is an amount effective to achieve a desired pharmacologic effect or therapeutic improvement without undue adverse side effects. It is understood that “an effect amount” or “a therapeutically effective amount” can vary from subject to subject, due to variation in metabolism of the compound of any of Formula (I)-(XXIIIh), age, weight, general condition of the subject, the condition being treated, the severity of the condition being treated, and the judgment of the prescribing physician. By way of example only, therapeutically effective amounts may be determined by routine experimentation, including but not limited to a dose escalation clinical trial.

The terms “enhance” or “enhancing” means to increase or prolong either in potency or duration a desired effect. By way of example, “enhancing” the effect of therapeutic agents refers to the ability to increase or prolong, either in potency or duration, the effect of therapeutic agents on during treatment of a disease, disorder or condition. An “enhancing-effective amount,” as used herein, refers to an amount adequate to enhance the effect of a therapeutic agent in the treatment of a disease, disorder or condition. When used in a patient, amounts effective for this use will depend on the severity and course of the disease, disorder or condition, previous therapy, the patient's health status and response to the drugs, and the judgment of the treating physician.

The term “identical,” as used herein, refers to two or more sequences or subsequences which are the same. In addition, the term “substantially identical,” as used herein, refers to two or more sequences which have a percentage of sequential units which are the same when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using comparison algorithms or by manual alignment and visual inspection. By way of example only, two or more sequences may be “substantially identical” if the sequential units are about 60% identical, about 65% identical, about 70% identical, about 75% identical, about 80% identical, about 85% identical, about 90% identical, or about 95% identical over a specified region. Such percentages to describe the “percent identity” of two or more sequences. The identity of a sequence can exist over a region that is at least about 75-100 sequential units in length, over a region that is about 50 sequential units in length, or, where not specified, across the entire sequence. This definition also refers to the complement of a test sequence. By way of example only, two or more polypeptide sequences are identical when the amino acid residues are the same, while two or more polypeptide sequences are “substantially identical” if the amino acid residues are about 60% identical, about 65% identical, about 70% identical, about 75% identical, about 80% identical, about 85% identical, about 90% identical, or about 95% identical over a specified region. The identity can exist over a region that is at least about 75-100 amino acids in length, over a region that is about 50 amino acids in length, or, where not specified, across the entire sequence of a polypeptide sequence. In addition, by way of example only, two or more polynucleotide sequences are identical when the nucleic acid residues are the same, while two or more polynucleotide sequences are “substantially identical” if the nucleic acid residues are about 60% identical, about 65% identical, about 70% identical, about 75% identical, about 80% identical, about 85% identical, about 90% identical, or about 95% identical over a specified region. The identity can exist over a region that is at least about 75-100 nucleic acids in length, over a region that is about 50 nucleic acids in length, or, where not specified, across the entire sequence of a polynucleotide sequence.

The term “isolated,” as used herein, refers to separating and removing a component of interest from components not of interest. Isolated substances can be in either a dry or semi-dry state, or in solution, including but not limited to an aqueous solution. The isolated component can be in a homogeneous state or the isolated component can be a part of a pharmaceutical composition that comprises additional pharmaceutically acceptable carriers and/or excipients. By way of example only, nucleic acids or proteins are “isolated” when such nucleic acids or proteins are free of at least some of the cellular components with which it is associated in the natural state, or that the nucleic acid or protein has been concentrated to a level greater than the concentration of its in vivo or in vitro production. Also, by way of example, a gene is isolated when separated from open reading frames which flank the gene and encode a protein other than the gene of interest.

A “metabolite” of a compound disclosed herein is a derivative of that compound that is formed when the compound is metabolized. The term “active metabolite” refers to a biologically active derivative of a compound that is formed when the compound is metabolized. The term “metabolized,” as used herein, refers to the sum of the processes (including, but not limited to, hydrolysis reactions and reactions catalyzed by enzymes, such as, oxidation reactions) by which a particular substance is changed by an organism. Thus, enzymes may produce specific structural alterations to a compound. For example, cytochrome P450 catalyzes a variety of oxidative and reductive reactions while uridine diphosphate glucuronyl transferases catalyze the transfer of an activated glucuronic-acid molecule to aromatic alcohols, aliphatic alcohols, carboxylic acids, amines and free sulfhydryl groups. Further information on metabolism may be obtained from The Pharmacological Basis of Therapeutics, 9th Edition, McGraw-Hill (1996). Metabolites of the compounds disclosed herein can be identified either by administration of compounds to a host and analysis of tissue samples from the host, or by incubation of compounds with hepatic cells in vitro and analysis of the resulting compounds. Both methods are well known in the art. In some embodiments, metabolites of a compound are formed by oxidative processes and correspond to the corresponding hydroxy-containing compound. In some embodiments, a compound is metabolized to pharmacologically active metabolites.

The term “modulate,” as used herein, means to interact with a target either directly or indirectly so as to alter the activity of the target, including, by way of example only, to enhance the activity of the target, to inhibit the activity of the target, to limit the activity of the target, or to extend the activity of the target.

As used herein, the term “modulator” refers to a compound that alters an activity of a molecule. For example, a modulator can cause an increase or decrease in the magnitude of a certain activity of a molecule compared to the magnitude of the activity in the absence of the modulator. In certain embodiments, a modulator is an inhibitor, which decreases the magnitude of one or more activities of a molecule. In certain embodiments, an inhibitor completely prevents one or more activities of a molecule. In certain embodiments, a modulator is an activator, which increases the magnitude of at least one activity of a molecule. In certain embodiments the presence of a modulator results in an activity that does not occur in the absence of the modulator.

The term “prophylactically effective amount,” as used herein, refers that amount of a composition applied to a patient that will relieve to some extent one or more of the symptoms of a disease, condition or disorder being treated. In such prophylactic applications, such amounts may depend on the patient's state of health, weight, and the like. It is considered well within the skill of the art for one to determine such prophylactically effective amounts by routine experimentation, including, but not limited to, a dose escalation clinical trial.

As used herein, the term “selective binding compound” refers to a compound that selectively binds to any portion of one or more target proteins.

As used herein, the term “selectively binds” refers to the ability of a selective binding compound to bind to a target protein, such as, for example, menin, with greater affinity than it binds to a non-target protein. In certain embodiments, specific binding refers to binding to a target with an affinity that is at least 10, 50, 100, 250, 500, 1000 or more times greater than the affinity for a non-target.

As used herein, the term “selective modulator” refers to a compound that selectively modulates a target activity relative to a non-target activity. In certain embodiments, specific modulator refers to modulating a target activity at least 10, 50, 100, 250, 500, 1000 times more than a non-target activity.

The term “substantially purified,” as used herein, refers to a component of interest that may be substantially or essentially free of other components which normally accompany or interact with the component of interest prior to purification. By way of example only, a component of interest may be “substantially purified” when the preparation of the component of interest contains less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 4%, less than about 3%, less than about 2%, or less than about 1% (by dry weight) of contaminating components. Thus, a “substantially purified” component of interest may have a purity level of about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or greater.

The term “subject” or “patient” as used herein, refers to an animal which is the object of treatment, observation or experiment. By way of example only, a subject may be, but is not limited to, a mammal including, but not limited to, a human.

As used herein, the term “target activity” refers to a biological activity capable of being modulated by a selective modulator. Certain exemplary target activities include, but are not limited to, binding affinity, signal transduction, enzymatic activity, tumor growth, inflammation or inflammation-related processes, and amelioration of one or more symptoms associated with a disease or condition.

As used herein, the term “target protein” refers to a molecule or a portion of a protein capable of being bound by a selective binding compound. In certain embodiments, a target protein is menin.

The terms “treat,” “treating” or “treatment”, as used herein, include alleviating, abating or ameliorating a disease or condition symptoms, preventing additional symptoms, ameliorating or preventing the underlying metabolic causes of symptoms, inhibiting the disease or condition, e.g., arresting the development of the disease or condition, relieving the disease or condition, causing regression of the disease or condition, relieving a condition caused by the disease or condition, or stopping the symptoms of the disease or condition. The terms “treat,” “treating” or “treatment”, include, but are not limited to, prophylactic and/or therapeutic treatments.

As used herein, the IC₅₀ refers to an amount, concentration or dosage of a particular test compound that achieves a 50% inhibition of a maximal response, such as inhibition of menin-MLL, in an assay that measures such response.

As used herein, EC₅₀ refers to a dosage, concentration or amount of a particular test compound that elicits a dose-dependent response at 50% of maximal expression of a particular response that is induced, provoked or potentiated by the particular test compound.

Methods described herein include administering to a subject in need a composition containing a therapeutically effective amount of one or more Menin-MLL inhibitor compounds described herein.

In some embodiments, methods described herein can be used to treat an autoimmune disease, which includes, but is not limited to, rheumatoid arthritis, psoriatic arthritis, osteoarthritis, Still's disease, juvenile arthritis, lupus, diabetes, myasthenia gravis, Hashimoto's thyroiditis, Ord's thyroiditis, Graves' disease Sjögren's syndrome, multiple sclerosis, Guillain-Barré syndrome, acute disseminated encephalomyelitis, Addison's disease, opsoclonus-myoclonus syndrome, ankylosing spondylitis, antiphospholipid antibody syndrome, aplastic anemia, autoimmune hepatitis, coeliac disease, Goodpasture's syndrome, idiopathic thrombocytopenic purpura, optic neuritis, scleroderma, primary biliary cirrhosis, Reiter's syndrome, Takayasu's arteritis, temporal arteritis, warm autoimmune hemolytic anemia, Wegener's granulomatosis, psoriasis, alopecia universalis, Beliefs disease, chronic fatigue, dysautonomia, endometriosis, interstitial cystitis, neuromyotonia, scleroderma, and vulvodynia.

In some embodiments, methods described herein can be used to treat heteroimmune conditions or diseases, which include, but are not limited to graft versus host disease, transplantation, transfusion, anaphylaxis, allergies (e.g., allergies to plant pollens, latex, drugs, foods, insect poisons, animal hair, animal dander, dust mites, or cockroach calyx), type I hypersensitivity, allergic conjunctivitis, allergic rhinitis, and atopic dermatitis.

In some embodiments, methods described herein can be used to treat an inflammatory disease, which includes, but is not limited to asthma, inflammatory bowel disease, appendicitis, blepharitis, bronchiolitis, bronchitis, bursitis, cervicitis, cholangitis, cholecystitis, colitis, conjunctivitis, cystitis, dacryoadenitis, dermatitis, dermatomyositis, encephalitis, endocarditis, endometritis, enteritis, enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis, gastritis, gastroenteritis, hepatitis, hidradenitis suppurativa, laryngitis, mastitis, meningitis, myelitis myocarditis, myositis, nephritis, oophoritis, orchitis, osteitis, otitis, pancreatitis, parotitis, pericarditis, peritonitis, pharyngitis, pleuritis, phlebitis, pneumonitis, pneumonia, proctitis, prostatitis, pyelonephritis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis, tendonitis, tonsillitis, uveitis, vaginitis, vasculitis, and vulvitis.

In some embodiments, methods described herein can be used to treat a cancer, e.g., B-cell proliferative disorders, which include, but are not limited to diffuse large B cell lymphoma, follicular lymphoma, chronic lymphocytic lymphoma, chronic lymphocytic leukemia, B-cell prolymphocytic leukemia, lymphoplasmacytic lymphoma/Waldenström macroglobulinemia, splenic marginal zone lymphoma, plasma cell myeloma, plasmacytoma, extranodal marginal zone B cell lymphoma, nodal marginal zone B cell lymphoma, mantle cell lymphoma, mediastinal (thymic) large B cell lymphoma, intravascular large B cell lymphoma, primary effusion lymphoma, burkitt lymphoma/leukemia, and lymphomatoid granulomatosis.

In some embodiments, methods described herein can be used to treat thromboembolic disorders, which include, but are not limited to myocardial infarct, angina pectoris (including unstable angina), reocclusions or restenoses after angioplasty or aortocoronary bypass, stroke, transitory ischemia, peripheral arterial occlusive disorders, pulmonary embolisms, and deep venous thromboses.

Symptoms, diagnostic tests, and prognostic tests for each of the above-mentioned conditions are known in the art. See, e.g., Harrison's Principles of Internal Medicine©,” 16th ed., 2004, The McGraw-Hill Companies, Inc. Dey et al. (2006), Cytojournal 3(24), and the “Revised European American Lymphoma” (REAL) classification system (see, e.g., the website maintained by the National Cancer Institute).

A number of animal models of are useful for establishing a range of therapeutically effective doses of Menin-MLL inhibitor compounds for treating any of the foregoing diseases.

For example, dosing of Menin-MLL inhibitor compounds for treating an autoimmune disease can be assessed in a mouse model of rheumatoid arthritis. In this model, arthritis is induced in Balb/c mice by administering anti-collagen antibodies and lipopolysaccharide. See Nandakumar et al. (2003), Am. J. Pathol 163:1827-1837.

In another example, dosing of Menin-MLL inhibitors for the treatment of B-cell proliferative disorders can be examined in, e.g., a human-to-mouse xenograft model in which human B-cell lymphoma cells (e.g. Ramos cells) are implanted into immunodeficient mice (e.g., “nude” mice) as described in, e.g., Pagel et al. (2005), Clin Cancer Res 11(13):4857-4866.

Animal models for treatment of thromboembolic disorders are also known.

The therapeutic efficacy of a provided compound for one of the foregoing diseases can be optimized during a course of treatment. For example, a subject being treated can undergo a diagnostic evaluation to correlate the relief of disease symptoms or pathologies to inhibition of in vivo menin-MLL activity achieved by administering a given dose of an Menin-MLL inhibitor.

Compounds

In the following description of Menin-MLL inhibitor compounds suitable for use in the methods described herein, definitions of referred-to standard chemistry terms may be found in reference works (if not otherwise defined herein), including Carey and Sundberg “Advanced Organic Chemistry 4th Ed.” Vols. A (2000) and B (2001), Plenum Press, New York. Unless otherwise indicated, conventional methods of mass spectroscopy, NMR, HPLC, protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the ordinary skill of the art are employedUnless specific definitions are provided, the nomenclature employed in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those known in the art. Standard techniques can be used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients.

Menin-MLL inhibitor compounds can be used for the manufacture of a medicament for treating any of the foregoing conditions (e.g., autoimmune diseases, inflammatory diseases, allergy disorders, B-cell proliferative disorders, Myeloid cell proliferative disorder, Lymphoid cell proliferative disorder, or thromboembolic disorders).

In some embodiments, the Menin-MLL inhibitor compound used for the methods described herein inhibits menin-MLL activity with an in vitro IC₅₀ of less than about 10 μM (e.g., less than about 1 μM, less than about 0.5 μM, less than about 0.4 μM, less than about 0.3 μM, less than about 0.1 μM, less than about 0.08 μM, less than about 0.06 μM, less than about 0.05 μM, less than about 0.04 μM, less than about 0.03 μM, less than about 0.02 μM, less than about 0.01 μM, less than about 0.008 μM, less than about 0.006 μM, less than about 0.005 μM, less than about 0.004 μM, less than about 0.003 μM, less than about 0.002 μM, less than about 0.001 μM, less than about 0.00099 μM, less than about 0.00098 μM, less than about 0.00097 μM, less than about 0.00096 μM, less than about 0.00095 μM, less than about 0.00094 μM, less than about 0.00093 μM, less than about 0.00092 μM, or less than about 0.00090 μM).

In some embodiments, the Menin-MLL inhibitor compound selectively inhibits an activated form of its target menin.

Described herein are compounds of any of Formulae (I), (IIa)-(IIb), (III), (IV), (V), (VI), (VII), (VIIIa)-(VIIId), or (IXa)-(IXd). Also described herein are pharmaceutically acceptable salts, pharmaceutically acceptable solvates, pharmaceutically active metabolites, and pharmaceutically acceptable prodrugs of such compounds. Pharmaceutical compositions that include at least one such compound or a pharmaceutically acceptable salt, pharmaceutically acceptable solvate, pharmaceutically active metabolite or pharmaceutically acceptable prodrug of such compound, are provided. In some embodiments, when compounds disclosed herein contain an oxidizable nitrogen atom, the nitrogen atom can be converted to an N-oxide by methods well known in the art. In certain embodiments, isomers and chemically protected forms of compounds having a structure represented by any of Formula (I)-(XXIIIh) are also provided.

In some embodiments, provided herein are menin-MLL inhibitors according to compounds of formula (I).

In some embodiments, the present invention provides a compound according to Formula (I) having the structure:

-   -   or a pharmaceutically acceptable salt thereof,     -   wherein:         A is O, or N(R^(6a));     -   Cy is substituted or unsubstituted

-   -   Q is —N(H)—, —O—, or —S—; Q′ is N, or C(H);     -   Z is —CR^(5a)═ or —N═;     -   one of X and Y is —NR^(3a)—; and the other is —C(R^(3b))₂—,         —NR^(3b)—, or —O—;     -   R¹ is an optionally substituted group selected from C₁₋₆ alkyl,         C₃₋₇ cycloalkyl, phenyl, an 8-10 membered bicyclic aryl ring, a         4-7 membered heterocycloalkyl ring having 1-2 heteroatoms         independently selected from nitrogen, oxygen, or sulfur, and a         5-6 membered heteroaryl ring having 1-4 heteroatoms         independently selected from nitrogen, oxygen, or sulfur;     -   R² is H, C₁₋₆ alkyl, C₁₋₆haloalkyl, halo, or CN;     -   each R^(3a), and R^(3b) is independently H or C₁₋₆ alkyl;     -   each R⁴ is independently H, halo, CN, OR, —N(R)₂, —C(O)N(R)₂,         —NRC(O)R, —SO₂R, —C(O)R, —CO₂R, or an optionally substituted         group selected from C₁₋₆ alkyl, C₃₋₇ cycloalkyl, a 4-7 membered         heterocycloalkyl ring having 1-2 heteroatoms independently         selected from nitrogen, oxygen, or sulfur, phenyl, an 8-10         membered bicyclic aryl ring, and a 5-6 membered heteroaryl ring         having 1-4 heteroatoms independently selected from nitrogen,         oxygen, or sulfur;     -   each R is independently H, or an optionally substituted group         selected from C₁₋₆ aliphatic, phenyl, an 8-10 membered bicyclic         aryl ring, a 4-7 membered saturated or partially unsaturated         heterocyclic ring having 1-2 heteroatoms independently selected         from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl         ring having 1-4 heteroatoms independently selected from         nitrogen, oxygen, or sulfur, or:     -   two R groups on the same nitrogen are taken together with their         intervening atoms to form a 4-7 membered saturated, partially         unsaturated, or heteroaryl ring having 0-3 heteroatoms, in         addition to the nitrogen, independently selected from nitrogen,         oxygen, or sulfur;     -   R^(5a) is H, C₁₋₆ alkyl, C₁₋₆haloalkyl, halo, or CN;     -   R^(6a) is H or and C₁₋₆ alkyl; and     -   n is 1, 2, 3, or 4.

In some embodiments, X is —NR^(3a)—; and Y is —C(R^(3b))₂—, —NR^(3b)—, or —O—.

In some embodiments, Y is —NR^(3a)—; and X is —C(R^(3b))₂—, —NR^(3b)—, or —O—.

In some embodiments, each of X and Y is independently —NR^(3a)—.

In some embodiments, R^(3a) is H.

In some embodiments, R^(3b) is H or Me.

In some embodiments, each of X and Y is —N(H)—.

In some embodiments, A is O.

In some embodiments, A is N(R^(6a)).

In some embodiments, R^(6a) is C₁₋₆alkyl.

In some embodiments, R^(6a) is Me, Et, or i-Pr.

In some embodiments, R^(6a) is H.

In particular embodiments, the compound is according to formula (IIa), (IIb), (IIe) or (IId):

or a pharmaceutically acceptable salt thereof wherein: Cy, R¹, R², R⁴, and n are as described herein.

In particular embodiments, the compound is according to formula (IIa′), or (IIb′)

or a pharmaceutically acceptable salt thereof, wherein: Cy, R¹, R², R⁴, A, and n are described herein.

In some embodiments, R² is H, C₁₋₆alkyl, C₁₋₆haloalkyl, halo, or CN.

In some embodiments, R² is H, Me, Et, i-Pr, CF₃, F, Cl, or CN.

In some embodiments, R² is H.

In particular embodiments, the compound is according to formula (IIIa), (IIIb), (IIIc) or (Did):

or a pharmaceutically acceptable salt thereof wherein: Cy, R¹, R⁴, and n are as described herein.

In some embodiments, n is 1, 2, 3, or 4.

In some embodiments, n is 1, 2, or 3.

In some embodiments, n is 1 or 2.

In some embodiments, n is 1.

In some embodiments, each R⁴ is independently H, halo, hydroxyl, CN, substituted or unsubstituted C₁₋₆alkyl, substituted or unsubstituted C₃₋₇ cycloalkyl, a substituted or unsubstituted 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

In some embodiments, each R⁴ is independently H, halo, hydroxyl, CN, substituted or unsubstituted C₁₋₆alkyl, substituted or unsubstituted amino, or substituted or unsubstituted alkoxy.

In some embodiments, each R⁴ is independently H, Me, Et, i-Pr, CF₃, F, Cl, OMe, OEt, or CN.

In some embodiments, each R⁴ is H.

In particular embodiments, the compound is according to formula (IIIa′), or (IIIb′):

or a pharmaceutically acceptable salt thereof wherein Cy, R¹, R⁴, and n are as described herein.

In some embodiments, A is O.

In some embodiments, A is N(R^(6a)).

In some embodiments, Cy is substituted or unsubstituted

In some embodiments, Cy is substituted or unsubstituted

In some embodiments, Q is —N(H)—. In some embodiments, Q′ is N.

In some embodiments, Q is —O—.

In some embodiments, Q is —S—.

In some embodiments, Z is —N═.

In some embodiments, Z is —CR^(5a)═.

In some embodiments, R^(5a) is H, Me, Et, i-Pr, Cl, F, CF₃, or CN.

In some embodiments, R^(5a) is H, Me, or F.

In some embodiments, R^(5a) is H.

In some embodiments, Z is —C(H)═.

In some embodiments, Cy is

wherein R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, phenyl, an 8-10 membered bicyclic aryl ring, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

In some embodiments, Cy is substituted or unsubstituted

wherein R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, phenyl, an 8-10 membered bicyclic aryl ring, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

In particular embodiments, the compound is according to formula (IVa), (IVb), (IVc) or (IVd):

or a pharmaceutically acceptable salt thereof wherein: R¹ is as described herein; and R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

In particular embodiments, the compound is according to formula (Va), (Vb), (Vc) or (Vd):

or a pharmaceutically acceptable salt thereof wherein: R¹ is as described herein; and R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

In particular embodiments, the compound is according to formula (VIa), (VIb), (VIc) or (VId):

wherein: R¹ is described herein; and R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound is according to formula (VIa′), (VIb′), (VIc′) or (VId′):

wherein: R¹ and R^(6a) are as described for formula (I); and R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (VIIa), (VIIb), (VIIe) or (VIId):

wherein: R¹ is as described herein; and R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; or a pharmaceutically acceptable salt thereof.

In some embodiments, the compound is according to formula (VIIa′), (VIIb′), (VIIe′) or (VIId′).

wherein: R¹ and R^(6a) are as in claim 1; and R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; or a pharmaceutically acceptable salt thereof.

In some embodiments, R¹ is substituted or unsubstituted C₁₋₆ alkyl.

In some embodiments, R¹ is substituted or unsubstituted Me, Et, or i-Pr.

In some embodiments, R¹ is Me, Et, CF₃, CHF₂, or C(Me)₂OH.

In some embodiments, R¹ is substituted or unsubstituted C₃₋₇ cycloalkyl, a substituted or unsubstituted 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

In some embodiments, R¹ is a substituted or unsubstituted 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

In some embodiments, R¹ is substituted or unsubstituted aryl.

In some embodiments, R¹ is substituted or unsubstituted heteroaryl.

In some embodiments, R¹ is substituted or unsubstituted pyrrolyl, furanyl, thienyl, pyrazolyl, imidazolyl, oxazolyl, isoxazolyl, thiazolyl, triazolyl, thiadiazolyl, pyridyl, pyrimidinyl, or pyrazinyl.

In some embodiments, R¹ is substituted or unsubstituted 2-pyridyl, 3-pyridyl or 4-pyridyl.

In some embodiments, the substitution on aryl or heteroaryl is selected from C₁₋₆alkyl, C₁₋₆haloalkyl, alkoxy, halo, and CN.

In some embodiments, the substitution on aryl or heteroaryl is selected from Me, Et, i-Pr, OMe, CF₃, F, Cl, and CN.

In some embodiments, R¹ is unsubstituted 2-pyridyl, 3-pyridyl or 4-pyridyl.

In some embodiments, R¹ is unsubstituted 3-pyridyl.

In some embodiments, R¹ is unsubstituted 3-pyridyl.

In some embodiments, R¹ is 3-methyl-4-pyridyl, 3-fluoro-4-pyridyl, or 3-cyano-4-pyridyl.

In some embodiments, R¹ is 4-methyl-3-pyridyl, 4-fluoro-3-pyridyl, or 4-cyano-3-pyridyl.

In some embodiments, R⁷ is 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur substituted with Me, Et, or i-Pr.

In some embodiments, R⁷ is pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl.

In some embodiments, R⁷ is morpholinyl.

In some embodiments, R⁷ is substituted or unsubstituted heteroaryl.

In some embodiments, R⁷ is substituted or unsubstituted pyridyl or pyrimidyl.

In some embodiments, R⁷ is unsubstituted pyridyl.

In some embodiments, R⁷ is pyridyl substituted with halo, hydroxyl, CN, substituted or unsubstituted C₁₋₆alkyl, substituted or unsubstituted amino, or substituted or unsubstituted alkoxy.

In some embodiments, R⁷ is pyridyl substituted with Me, Et, i-Pr, OH, Cl, F, CF₃, CN, or NH₂.

In some embodiments, R⁷ is pyridyl substituted with Me, Et, i-Pr, Cl, F, CF₃, or CN.

In some embodiments, R⁷ is substituted or unsubstituted pyrrolyl, pyrazolyl, imidazolyl, oxazolyl, triazolyl, thiazolyl, oxadiazolyl, or thiadiazolyl.

In some embodiments, R⁷ is substituted or unsubstituted imidazolyl.

In some embodiments, R⁷ is imidazoyl substituted with Me, Et, i-Pr, Cl, F, CF₃, or CN.

In some embodiments, R⁷ is imidazoyl substituted with Me.

In some embodiments, R^(6a) is C₁₋₆alkyl.

In some embodiments, R^(6a) is Me, Et, or i-Pr.

In some embodiments, R^(6a) is H.

In particular embodiments, the compound is according to formula (VIIIa), (VIIIb), (VIIIc) or (VIIId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (IXa), (IXb), (IXc) or (IXd):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (Xa), (Xb), (Xc) or (Xd):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (Xe), (Xf), (Xg) or (Xh):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIa), (XIb), (XIc) or (XId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIe), (XIf), (XIg) or (XIh):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIIa), (XIIb), (XIIc) or (XIId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIIIa), (XIIIb), (XIIIc) or (XIIId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIVa), (XIVb), (XIVc) or (XIVd):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIVe), (XIVf), (XIVg) or (XIVh):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XVa), (XVb), (XVc) or (XVd):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XVe), (XVf), (XVg) or (XVh):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XVIa), (XVIb), (XVIc) or (XVId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XVIIa), (XVIIb), (XVIIc) or (XVIId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XVIIIa), (XVIIIb), (XVIIIc) or (XVIIId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XVIIIe), (XVIIIf), (XVIIIg) or (XVIIIh):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIXa), (XIXb), (XIXc) or (XIXd):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIXe), (XIXf), (XIXg) or (XIXh):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XXa), (XXb), (XXc) or (XXd):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XXIa), (XXIb), (XXIc) or (XXId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XXIIa), (XXIIb), (XXIIc) or (XXIId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XXIIe), (XXIIf), (XXIIg) or (XXIIh):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XXIIIa), (XXIIIb), (XXIIIc) or (XXIIId):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XXIIIe), (XXIIIf), (XXIIIg) or (XXIIIh):

or a pharmaceutically acceptable salt thereof

In particular embodiments, the compound is according to formula (VIIIb):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIYb):

or a pharmaceutically acceptable salt thereof.

In particular embodiments, the compound is according to formula (XIYf):

or a pharmaceutically acceptable salt thereof.

Embodiments of the compounds of Formula (I) displayed improved potency against menin-MLL with IC₅₀ values of as low as less than 1 nM or less than 0.1 nM, and/or high occupancy of active site of menin (e.g., more than 50%, 70% or 90% occupancy) at low dosages of below 5 mg/kg (e.g., at or below 3 mg/kg) when administered in vivo (e.g., in rats).

In some embodiments, the present invention provides, a pharmaceutical composition comprising a compound according to formula (I).

In some embodiments, the present invention provides, a pharmaceutical composition comprising a therapeutically effective amount of a compound of formula (I), and a pharmaceutically acceptable excipient.

In some embodiments, the pharmaceutical composition is formulated for a route of administration selected from oral administration, parenteral administration, buccal administration, nasal administration, topical administration, or rectal administration.

In some embodiments, the present invention provides, methods for treating an autoimmune disease or condition comprising administering to a patient in need the pharmaceutical composition of the present invention.

In some embodiments, the autoimmune disease is selected from rheumatoid arthritis or lupus.

In some embodiments, the present invention provides, methods for treating a heteroimmune disease or condition comprising administering to a patient in need the pharmaceutical composition of the present invention.

In some embodiments, the present invention provides, for treating a cancer comprising administering to a patient in need the pharmaceutical composition the present invention.

In some embodiments, the cancer is a B-cell proliferative disorder.

In some embodiments, the B-cell proliferative disorder is diffuse large B cell lymphoma, follicular lymphoma or chronic lymphocytic leukemia. In some embodiments, the disorder is Myeloid leukemia. In some embodiments, the disorder is AML. In some embodiments, the B-cell proliferative disorder is Lymphoid leukemia. In some embodiments, the disorder is ALL. In some embodiments, the disorder is Soft Tissue tumors. In some embodiments, the tumor is Glioblastoma. In some embodiments, the tumor is pancreatic tumor. In some embodiments, the disorder is Renal Cell Cancer.

In some embodiments, the present invention provides, methods for treating mastocytosis comprising administering to a patient in need the pharmaceutical composition of the present invention.

In some embodiments, the present invention provides, methods for treating osteoporosis or bone resorption disorders comprising administering to a patient in need the pharmaceutical composition of the present invention.

In some embodiments, the present invention provides, methods or treating an inflammatory disease or condition comprising administering to a patient in need the pharmaceutical composition of the present invention.

In some embodiments, the present invention provides, methods for treating lupus comprising administering to a subject in need thereof a composition containing a therapeutically effective amount of a compound of formula (I) that is inhibitor of menin-MLL interaction.

In some embodiments, the present invention provides methods for treating a heteroimmune disease or condition comprising administering to a subject in need thereof a composition containing a therapeutically effective amount of a compound of formula (I) that is inhibitor of menin-MLL interaction.

In some embodiments, the present invention provides, methods for treating diffuse large B cell lymphoma, follicular lymphoma or chronic lymphocytic leukemia comprising administering to a subject in need thereof a composition containing a therapeutically effective amount of a compound of formula (I) that is inhibitor of the menin-MLL interaction.

In some embodiments, the present invention provides methods for treating mastocytosis, comprising administering to a subject in need thereof a composition containing a therapeutically effective amount of a compound of formula (I) that is inhibitor of menin-MLL interaction.

In some embodiments, the present invention provides methods for treating osteoporosis or bone resorption disorders comprising administering to a subject in need thereof a composition containing a therapeutically effective amount of a compound of formula (I) that is inhibitor of menin-MLL interaction.

In some embodiments, the present invention provides methods for treating an inflammatory disease or condition comprising administering to a subject in need thereof a composition containing a therapeutically effective amount of a compound of formula (I) that is inhibitor of menin-MLL interaction.

In some embodiments, the present invention provides, a pharmaceutical composition comprising a pharmaceutically acceptable carrier and a pharmaceutically effective amount of a compound according to any one of the formulas described herein. In some embodiments, the compound is according to any one of Formula (I)-(XXIIIh).

In some embodiments, the pharmaceutical composition is formulated for a route of administration selected from oral administration, parenteral administration, buccal administration, nasal administration, topical administration, or rectal administration.

In some embodiments, the carrier is a parenteral carrier.

In some embodiments, the carrier is an oral carrier.

In some embodiments, the carrier is a topical carrier.

Any combination of the groups described above for the various variables is contemplated herein. It is understood that substituents and substitution patterns on the compounds provided herein can be selected by one of ordinary skill in the art to provide compounds that are chemically stable and that can be synthesized by techniques known in the art, as well as those set forth herein.

Further representative embodiments of compounds of Formula (I), include compounds of the following formulae:

or a solvate or a pharmaceutically acceptable salt thereof.

In some embodiments, with respect to the above listed compounds, R is halo. In some embodiments, R is CN. In yet some embodiments, R is cyclopropyl.

Throughout the specification, groups and substituents thereof can be chosen by one skilled in the field to provide stable moieties and compounds.

In some embodiments, the compounds of Formula (I)-(XXIIIh) inhibit menin-MLL. In some embodiments, the compounds of Formula (I)-(XXIIIh) are used to treat patients suffering from menin-MLL-dependent or menin-MLL interaction mediated conditions or diseases, including, but not limited to, cancer, autoimmune and other inflammatory diseases.

In some embodiments, the compounds of Formula (I)-(XXIIIh) inhibit menin-MLL interaction. In some embodiments, the compounds of Formula (I)-(XXIIIh) are used to treat patients suffering from menin-MLL interaction-dependent or menin-MLL interaction mediated conditions or diseases, including, but not limited to, cancer, autoimmune and other inflammatory diseases.

Preparation of Compounds

Compounds of any of Formula (I)-(XXIIIh) may be synthesized using standard synthetic reactions known to those of skill in the art or using methods known in the art. The reactions can be employed in a linear sequence to provide the compounds or they may be used to synthesize fragments which are subsequently joined by the methods known in the art.

Described herein are compounds that inhibit the activity of menin-MLL, and processes for their preparation. Also described herein are pharmaceutically acceptable salts, pharmaceutically acceptable solvates, pharmaceutically active metabolites and pharmaceutically acceptable prodrugs of such compounds. Pharmaceutical compositions that include at least one such compound or a pharmaceutically acceptable salt, pharmaceutically acceptable solvate, pharmaceutically active metabolite or pharmaceutically acceptable prodrug of such compound, are provided.

The starting material used for the synthesis of the compounds described herein may be synthesized or can be obtained from commercial sources, such as, but not limited to, Aldrich Chemical Co. (Milwaukee, Wis.), Bachem (Torrance, Calif.), or Sigma Chemical Co. (St. Louis, Mo.). The compounds described herein, and other related compounds having different substituents can be synthesized using techniques and materials known to those of skill in the art, such as described, for example, in March, ADVANCED ORGANIC CHEMISTRY 4^(th) Ed., (Wiley 1992); Carey and Sundberg, ADVANCED ORGANIC CHEMISTRY 4^(th) Ed., Vols. A and B (Plenum 2000, 2001); Green and Wuts, PROTECTIVE GROUPS IN ORGANIC SYNTHESIS 3^(rd) Ed., (Wiley 1999); Fieser and Fieser's Reagents for Organic Synthesis, Volumes 1-17 (John Wiley and Sons, 1991); Rodd's Chemistry of Carbon Compounds, Volumes 1-5 and Supplemental (Elsevier Science Publishers, 1989); Organic Reactions, Volumes 1-40 (John Wiley and Sons, 1991); and Larock's Comprehensive Organic Transformations (VCH Publishers Inc., 1989) (all of which are incorporated by reference in their entirety). Additional methods for the synthesis of compounds described herein may be found in International Patent Publication No. WO 01/01982901, Arnold et al. Bioorganic & Medicinal Chemistry Letters 10 (2000) 2167-2170; Burchat et al. Bioorganic & Medicinal Chemistry Letters 12 (2002) 1687-1690. General methods for the preparation of compound as disclosed herein may be derived from known reactions in the field, and the reactions may be modified by the use of appropriate reagents and conditions, as would be recognized by the skilled person, for the introduction of the various moieties found in the formulae as provided herein.

The products of the reactions may be isolated and purified, if desired, using conventional techniques, including, but not limited to, filtration, distillation, crystallization, chromatography and the like. Such materials may be characterized using conventional means, including physical constants and spectral data.

Compounds described herein may be prepared as a single isomer or a mixture of isomers.

In some embodiments, representative compounds of Formula (I) are prepared according to synthetic schemes depicted herein.

Further Forms of Compounds

Compounds disclosed herein have a structure of Formula (I)-(XXIIIh). It is understood that when reference is made to compounds described herein, it is meant to include compounds of any of Formula (I)-(XXIIIh) as well as to all of the specific compounds that fall within the scope of these generic formulae, unless otherwise indicated.

Compounds described herein may possess one or more stereocenters and each center may exist in the R or S configuration. Compounds presented herein include all diastereomeric, enantiomeric, and epimeric forms as well as the appropriate mixtures thereof. Stereoisomers may be obtained, if desired, by methods known in the art as, for example, the separation of stereoisomers by chiral chromatographic columns.

Diastereomeric mixtures can be separated into their individual diastereomers on the basis of their physical chemical differences by methods known, for example, by chromatography and/or fractional crystallization. In some embodiments, enantiomers can be separated by chiral chromatographic columns. In some embodiments, enantiomers can be separated by converting the enantiomeric mixture into a diastereomeric mixture by reaction with an appropriate optically active compound (e.g., alcohol), separating the diastereomers and converting (e.g., hydrolyzing) the individual diastereomers to the corresponding pure enantiomers. All such isomers, including diastereomers, enantiomers, and mixtures thereof are considered as part of the compositions described herein.

Methods and formulations described herein include the use of A-ox ides, crystalline forms (also known as polymorphs), or pharmaceutically acceptable salts of compounds described herein, as well as active metabolites of these compounds having the same type of activity. In some situations, compounds may exist as tautomers. All tautomers are included within the scope of the compounds presented herein. In addition, compounds described herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. Solvated forms of compounds presented herein are also considered to be disclosed herein.

Compounds of any of Formula (I)-(XXIIIh) in unoxidized form can be prepared from N-oxides of compounds of any of Formula (I)-(XXIIIh) by treating with a reducing agent, such as, but not limited to, sulfur, sulfur dioxide, triphenyl phosphine, lithium borohydride, sodium borohydride, phosphorus trichloride, tribromide, or the like in a suitable inert organic solvent, such as, but not limited to, acetonitrile, ethanol, aqueous dioxane, or the like at 0 to 80° C.

In some embodiments, compounds described herein are prepared as prodrugs. A “prodrug” refers to an agent that is converted into the parent drug in vivo. Prodrugs are often useful because, in some situations, they may be easier to administer than the parent drug. They may, for instance, be bioavailable by oral administration whereas the parent is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug. An example, without limitation, of a prodrug would be a compound described herein, which is administered as an ester (the “prodrug”) to facilitate transmittal across a cell membrane where water solubility is detrimental to mobility but which then is metabolically hydrolyzed to the carboxylic acid, the active entity, once inside the cell where water-solubility is beneficial. A further example of a prodrug might be a short peptide (polyaminoacid) bonded to an acid group where the peptide is metabolized to reveal the active moiety. In certain embodiments, upon in vivo administration, a prodrug is chemically converted to the biologically, pharmaceutically or therapeutically active form of the compound. In certain embodiments, a prodrug is enzymatically metabolized by one or more steps or processes to the biologically, pharmaceutically or therapeutically active form of the compound. To produce a prodrug, a pharmaceutically active compound is modified such that the active compound will be regenerated upon in vivo administration. The prodrug can be designed to alter the metabolic stability or the transport characteristics of a drug, to mask side effects or toxicity, to improve the flavor of a drug or to alter other characteristics or properties of a drug. By virtue of knowledge of pharmacodynamic processes and drug metabolism in vivo, those of skill in this art, once a pharmaceutically active compound is known, can design prodrugs of the compound, (see, for example, Nogrady (1985) Medicinal Chemistry A Biochemical Approach, Oxford University Press, New York, pages 388-392; Silverman (1992), The Organic Chemistry of Drug Design and Drug Action, Academic Press, Inc., San Diego, pages 352-401, Saulnier et al., (1994), Bioorganic and Medicinal Chemistry Letters, Vol. 4, p. 1985).

Prodrug forms of the herein described compounds, wherein the prodrug is metabolized in vivo to produce a derivative as set forth herein are included within the scope of the claims. In some cases, some of the herein-described compounds may be a prodrug for another derivative or active compound.

Prodrugs are often useful because, in some situations, they may be easier to administer than the parent drug. They may, for instance, be bioavailable by oral administration whereas the parent is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug. Prodrugs may be designed as reversible drug derivatives, for use as modifiers to enhance drug transport to site-specific tissues. In some embodiments, the design of a prodrug increases the effective water solubility. See, e.g., Fedorak et al., Am. J. Physiol., 269:G210-218 (1995); McLoed et al., Gastroenterol, 106:405-413 (1994); Hochhaus et al., Biomed. Chrom., 6:283-286 (1992); J. Larsen and H. Bundgaard, Int. J. Pharmaceutics, 37, 87 (1987); J. Larsen et al., Int. J. Pharmaceutics, 47, 103 (1988); Sinkula et al., J. Pharm. Sci., 64:181-210 (1975); T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems, Vol. 14 of the A.C.S. Symposium Series; and Edward B. Roche, Bioreversible Carriers in Drug Design, American Pharmaceutical Association and Pergamon Press, 1987, all incorporated herein in their entirety.

Sites on the aromatic ring portion of compounds of any of Formula (I)-(XXIIIh) can be susceptible to various metabolic reactions, therefore incorporation of appropriate substituents on the aromatic ring structures, such as, by way of example only, halogens can reduce, minimize or eliminate this metabolic pathway.

Compounds described herein include isotopically-labeled compounds, which are identical to those recited in the various formulas and structures presented herein, but for the fact that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number usually found in nature. Examples of isotopes that can be incorporated into the present compounds include isotopes of hydrogen, carbon, nitrogen, oxygen, fluorine and chlorine, such as ²H, ³H, ¹³C, ¹⁴C, ¹⁵N, ¹⁸O, ¹⁷O, ³⁵S, ¹⁸F, ³⁶Cl, respectively. Certain isotopically-labeled compounds described herein, for example those into which radioactive isotopes such as ³H and ¹⁴C are incorporated, are useful in drug and/or substrate tissue distribution assays. Further, substitution with isotopes such as deuterium, i.e., ²H, can afford certain therapeutic advantages resulting from greater metabolic stability, for example increased in vivo half-life or reduced dosage requirements.

In additional or some embodiments, the compounds described herein are metabolized upon administration to an organism in need to produce a metabolite that is then used to produce a desired effect, including a desired therapeutic effect.

Compounds described herein may be formed as, and/or used as, pharmaceutically acceptable salts. The type of pharmaceutical acceptable salts, include, but are not limited to: (1) acid addition salts, formed by reacting the free base form of the compound with a pharmaceutically acceptable: inorganic acid such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, metaphosphoric acid, and the like; or with an organic acid such as acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, trifluoroacetic acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, toluenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4′-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like; (2) salts formed when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion (e.g. lithium, sodium, potassium), an alkaline earth ion (e.g. magnesium, or calcium), or an aluminum ion; or coordinates with an organic base. Acceptable organic bases include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases include aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like.

The corresponding counterions of the pharmaceutically acceptable salts may be analyzed and identified using various methods including, but not limited to, ion exchange chromatography, ion chromatography, capillary electrophoresis, inductively coupled plasma, atomic absorption spectroscopy, mass spectrometry, or any combination thereof.

The salts are recovered by using at least one of the following techniques: filtration, precipitation with a non-solvent followed by filtration, evaporation of the solvent, or, in the case of aqueous solutions, lyophilization.

It should be understood that a reference to a pharmaceutically acceptable salt includes the solvent addition forms or crystal forms thereof, particularly solvates or polymorphs. Solvates contain either stoichiometric or non-stoichiometric amounts of a solvent, and may be formed during the process of crystallization with pharmaceutically acceptable solvents such as water, ethanol, and the like. Hydrates are formed when the solvent is water, or alcoholates are formed when the solvent is alcohol. Solvates of compounds described herein can be conveniently prepared or formed during the processes described herein. In addition, the compounds provided herein can exist in unsolvated as well as solvated forms. In general, the solvated forms are considered equivalent to the unsolvated forms for the purposes of the compounds and methods provided herein.

It should be understood that a reference to a salt includes the solvent addition forms or crystal forms thereof, particularly solvates or polymorphs. Solvates contain either stoichiometric or non-stoichiometric amounts of a solvent, and are often formed during the process of crystallization with pharmaceutically acceptable solvents such as water, ethanol, and the like. Hydrates are formed when the solvent is water, or alcoholates are formed when the solvent is alcohol. Polymorphs include the different crystal packing arrangements of the same elemental composition of a compound. Polymorphs usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Various factors such as the recrystallization solvent, rate of crystallization, and storage temperature may cause a single crystal form to dominate.

Compounds described herein may be in various forms, including but not limited to, amorphous forms, milled forms and nano-particulate forms. In addition, compounds described herein include crystalline forms, also known as polymorphs. Polymorphs include the different crystal packing arrangements of the same elemental composition of a compound. Polymorphs usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Various factors such as the recrystallization solvent, rate of crystallization, and storage temperature may cause a single crystal form to dominate.

The screening and characterization of the pharmaceutically acceptable salts, polymorphs and/or solvates may be accomplished using a variety of techniques including, but not limited to, thermal analysis, x-ray diffraction, spectroscopy, vapor sorption, and microscopy. Thermal analysis methods address thermo chemical degradation or thermo physical processes including, but not limited to, polymorphic transitions, and such methods are used to analyze the relationships between polymorphic forms, determine weight loss, to find the glass transition temperature, or for excipient compatibility studies. Such methods include, but are not limited to, Differential scanning calorimetry (DSC), Modulated Differential Scanning Calorimetry (MDCS), Thermogravimetric analysis (TGA), and Thermogravi-metric and Infrared analysis (TG/IR). X-ray diffraction methods include, but are not limited to, single crystal and powder diffractometers and synchrotron sources. The various spectroscopic techniques used include, but are not limited to, Raman, FTIR, UVIS, and NMR (liquid and solid state). The various microscopy techniques include, but are not limited to, polarized light microscopy, Scanning Electron Microscopy (SEM) with Energy Dispersive X-Ray Analysis (EDX), Environmental Scanning Electron Microscopy with EDX (in gas or water vapor atmosphere), IR microscopy, and Raman microscopy.

Throughout the specification, groups and substituents thereof can be chosen by one skilled in the field to provide stable moieties and compounds.

Pharmaceutical Composition/Formulation

Pharmaceutical compositions may be formulated in a conventional manner using one or more physiologically acceptable carriers including excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen. Any of the well-known techniques, carriers, and excipients may be used as suitable and as understood in the art. A summary of pharmaceutical compositions described herein may be found, for example, in Remington; The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 1975; Liberman, H. A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N.Y., 1980; and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins 1999), herein incorporated by reference in their entirety.

A pharmaceutical composition, as used herein, refers to a mixture of a compound described herein, such as, for example, compounds of any of Formula (I)-(XXIIIh) with other chemical components, such as carriers, stabilizers, diluents, dispersing agents, suspending agents, thickening agents, and/or excipients. The pharmaceutical composition facilitates administration of the compound to an organism. In practicing the methods of treatment or use provided herein, therapeutically effective amounts of compounds described herein are administered in a pharmaceutical composition to a mammal having a disease, disorder, or condition to be treated. Preferably, the mammal is a human. A therapeutically effective amount can vary widely depending on the severity of the disease, the age and relative health of the subject, the potency of the compound used and other factors. The compounds can be used singly or in combination with one or more therapeutic agents as components of mixtures.

In certain embodiments, compositions may also include one or more pH adjusting agents or buffering agents, including acids such as acetic, boric, citric, lactic, phosphoric and hydrochloric acids; bases such as sodium hydroxide, sodium phosphate, sodium borate, sodium citrate, sodium acetate, sodium lactate and tris-hydroxymethylaminomethane; and buffers such as citrate/dextrose, sodium bicarbonate and ammonium chloride. Such acids, bases and buffers are included in an amount required to maintain pH of the composition in an acceptable range.

In some embodiments, compositions may also include one or more salts in an amount required to bring osmolality of the composition into an acceptable range. Such salts include those having sodium, potassium or ammonium cations and chloride, citrate, ascorbate, borate, phosphate, bicarbonate, sulfate, thiosulfate or bisulfite anions; suitable salts include sodium chloride, potassium chloride, sodium thiosulfate, sodium bisulfite and ammonium sulfate.

The term “pharmaceutical combination” as used herein, means a product that results from the mixing or combining of more than one active ingredient and includes both fixed and non-fixed combinations of the active ingredients. The term “fixed combination” means that the active ingredients, e.g. a compound described herein and a co-agent, are both administered to a patient simultaneously in the form of a single entity or dosage. The term “non-fixed combination” means that the active ingredients, e.g. a compound described herein and a co-agent, are administered to a patient as separate entities either simultaneously, concurrently or sequentially with no specific intervening time limits, wherein such administration provides effective levels of the two compounds in the body of the patient. The latter also applies to cocktail therapy, e.g. the administration of three or more active ingredients.

The pharmaceutical compositions described herein can be administered to a subject by multiple administration routes, including but not limited to, oral, parenteral (e.g., intravenous, subcutaneous, intramuscular), intranasal, buccal, topical, rectal, or transdermal administration routes. The pharmaceutical compositions described herein include, but are not limited to, aqueous liquid dispersions, self-emulsifying dispersions, solid solutions, liposomal dispersions, aerosols, solid dosage forms, powders, immediate release formulations, controlled release formulations, fast melt formulations, tablets, capsules, pills, delayed release formulations, extended release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate and controlled release formulations.

Pharmaceutical compositions including a compound described herein may be manufactured in a conventional manner, such as, by way of example only, by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or compression processes.

The pharmaceutical compositions will include at least one compound described herein, such as, for example, a compound of any of Formula (I)-(XXIIIh) as an active ingredient in free-acid or free-base form, or in a pharmaceutically acceptable salt form. In addition, the methods and pharmaceutical compositions described herein include the use of A-oxides, crystalline forms (also known as polymorphs), as well as active metabolites of these compounds having the same type of activity. In some situations, compounds may exist as tautomers. All tautomers are included within the scope of the compounds presented herein. Additionally, the compounds described herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. The solvated forms of the compounds presented herein are also considered to be disclosed herein.

“Antifoaming agents” reduce foaming during processing which can result in coagulation of aqueous dispersions, bubbles in the finished film, or generally impair processing. Exemplary anti-foaming agents include silicon emulsions or sorbitan sesquoleate.

“Antioxidants” include, for example, butylated hydroxytoluene (BHT), sodium ascorbate, ascorbic acid, sodium metabisulfite and tocopherol. In certain embodiments, antioxidants enhance chemical stability where required.

In certain embodiments, compositions provided herein may also include one or more preservatives to inhibit microbial activity. Suitable preservatives include mercury-containing substances such as merfen and thiomersal; stabilized chlorine dioxide; and quaternary ammonium compounds such as benzalkonium chloride, cetyltrimethylammonium bromide and cetylpyridinium chloride.

Formulations described herein may benefit from antioxidants, metal chelating agents, thiol containing compounds and other general stabilizing agents. Examples of such stabilizing agents, include, but are not limited to: (a) about 0.5% to about 2% w/v glycerol, (b) about 0.1% to about 1% w/v methionine, (c) about 0.1% to about 2% w/v monothioglycerol, (d) about 1 mM to about 10 mM EDTA, (e) about 0.01% to about 2% w/v ascorbic acid, (f) 0.003% to about 0.02% w/v polysorbate 80, (g) 0.001% to about 0.05% w/v. polysorbate 20, (h) arginine, (i) heparin, (j) dextran sulfate, (k) cyclodextrins, (l) pentosan polysulfate and other heparinoids, (m) divalent cations such as magnesium and zinc; or (n) combinations thereof.

“Binders” impart cohesive qualities and include, e.g., alginic acid and salts thereof; cellulose derivatives such as carboxymethylcellulose, methylcellulose (e.g., Methocel®), hydroxypropylmethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose (e.g., Klucel®), ethylcellulose (e.g., Ethocel®), and microcrystalline cellulose (e.g., Avicel®); microcrystalline dextrose; amylose; magnesium aluminum silicate; polysaccharide acids; bentonites; gelatin; polyvinylpyrrolidone/vinyl acetate copolymer; crosspovidone; povidone; starch; pregelatinized starch; tragacanth, dextrin, a sugar, such as sucrose (e.g., Dipac®), glucose, dextrose, molasses, mannitol, sorbitol, xylitol (e.g., Xylitab®), and lactose; a natural or synthetic gum such as acacia, tragacanth, ghatti gum, mucilage of isapol husks, polyvinylpyrrolidone (e.g., Polyvidone® CL, Kollidon® CL, Polyplasdone® XL-10), larch arabogalactan, Veegum®, polyethylene glycol, waxes, sodium alginate, and the like.

A “carrier” or “carrier materials” include any commonly used excipients in pharmaceutics and should be selected on the basis of compatibility with compounds disclosed herein, such as, compounds of any of Formula (I)-(XXIIIh) and the release profile properties of the desired dosage form. Exemplary carrier materials include, e.g., binders, suspending agents, disintegration agents, filling agents, surfactants, solubilizers, stabilizers, lubricants, wetting agents, diluents, and the like. “Pharmaceutically compatible carrier materials” may include, but are not limited to, acacia, gelatin, colloidal silicon dioxide, calcium glycerophosphate, calcium lactate, maltodextrin, glycerine, magnesium silicate, polyvinylpyrrollidone (PVP), cholesterol, cholesterol esters, sodium caseinate, soy lecithin, taurocholic acid, phosphotidylcholine, sodium chloride, tricalcium phosphate, dipotassium phosphate, cellulose and cellulose conjugates, sugars sodium stearoyl lactylate, carrageenan, monoglyceride, diglyceride, pregelatinized starch, and the like. See, e.g., Remington; The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 1975; Liberman, H. A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N.Y., 1980; and Pharmaceutical Dosage Norms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins 1999).

“Dispersing agents,” and/or “viscosity modulating agents” include materials that control the diffusion and homogeneity of a drug through liquid media or a granulation method or blend method. In some embodiments, these agents also facilitate the effectiveness of a coating or eroding matrix. Exemplary diffusion facilitators/dispersing agents include, e.g., hydrophilic polymers, electrolytes, Tween® 60 or 80, PEG, polyvinylpyrrolidone (PVP; commercially known as Plasdone®), and the carbohydrate-based dispersing agents such as, for example, hydroxypropyl celluloses (e.g., HPC, HPC-SL, and HPC-L), hydroxypropyl methylcelluloses (e.g., HPMC K100, HPMC K4M, HPMC K15M, and HPMC K100M), carboxymethylcellulose sodium, methylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropylmethylcellulose phthalate, hydroxypropylmethylcellulose acetate stearate (HPMCAS), noncrystalline cellulose, magnesium aluminum silicate, triethanolamine, polyvinyl alcohol (PVA), vinyl pyrrolidone/vinyl acetate copolymer (S630), 4-(1,1,3,3-tetramethylbutyl)-phenol polymer with ethylene oxide and formaldehyde (also known as tyloxapol), poloxamers (e.g., Pluronics F68®, F88®, and F108®, which are block copolymers of ethylene oxide and propylene oxide); and poloxamines (e.g., Tetronic 908®, also known as Poloxamine 908®, which is a tetrafunctional block copolymer derived from sequential addition of propylene oxide and ethylene oxide to ethylenediamine (BASF Corporation, Parsippany, N.J.)), polyvinylpyrrolidone K12, polyvinylpyrrolidone K17, polyvinylpyrrolidone K25, or polyvinylpyrrolidone K30, polyvinylpyrrolidone/vinyl acetate copolymer (S-630), polyethylene glycol, e.g., the polyethylene glycol can have a molecular weight of about 300 to about 6000, or about 3350 to about 4000, or about 7000 to about 5400, sodium carboxymethylcellulose, methylcellulose, polysorbate-80, sodium alginate, gums, such as, e.g., gum tragacanth and gum acacia, guar gum, xanthans, including xanthan gum, sugars, cellulosics, such as, e.g., sodium carboxymethylcellulose, methylcellulose, sodium carboxymethylcellulose, polysorbate-80, sodium alginate, polyethoxylated sorbitan monolaurate, polyethoxylated sorbitan monolaurate, povidone, carbomers, polyvinyl alcohol (PVA), alginates, chitosans and combinations thereof. Plasticizcers such as cellulose or triethyl cellulose can also be used as dispersing agents. Dispersing agents particularly useful in liposomal dispersions and self-emulsifying dispersions are dimyristoyl phosphatidyl choline, natural phosphatidyl choline from eggs, natural phosphatidyl glycerol from eggs, cholesterol and isopropyl myristate.

Combinations of one or more erosion facilitator with one or more diffusion facilitator can also be used in the present compositions.

The term “diluent” refers to chemical compounds that are used to dilute the compound of interest prior to delivery. Diluents can also be used to stabilize compounds because they can provide a more stable environment. Salts dissolved in buffered solutions (which also can provide pH control or maintenance) are utilized as diluents in the art, including, but not limited to a phosphate buffered saline solution. In certain embodiments, diluents increase bulk of the composition to facilitate compression or create sufficient bulk for homogenous blend for capsule filling. Such compounds include e.g., lactose, starch, mannitol, sorbitol, dextrose, microcrystalline cellulose such as Avicel®; dibasic calcium phosphate, dicalcium phosphate dihydrate; tricalcium phosphate, calcium phosphate; anhydrous lactose, spray-dried lactose; pregelatinized starch, compressible sugar, such as Di-Pac® (Amstar); mannitol, hydroxypropylmethylcellulose, hydroxypropylmethylcellulose acetate stearate, sucrose-based diluents, confectioner's sugar; monobasic calcium sulfate monohydrate, calcium sulfate dihydrate; calcium lactate trihydrate, dextrates; hydrolyzed cereal solids, amylose; powdered cellulose, calcium carbonate; glycine, kaolin; mannitol, sodium chloride; inositol, bentonite, and the like.

The term “disintegrate” includes both the dissolution and dispersion of the dosage form when contacted with gastrointestinal fluid. “Disintegration agents or disintegrants” facilitate the breakup or disintegration of a substance. Examples of disintegration agents include a starch, e.g., a natural starch such as corn starch or potato starch, a pregelatinized starch such as National 1551 or Amijel®, or sodium starch glycolate such as Promogel® or Explotab®, a cellulose such as a wood product, methylcrystalline cellulose, e.g., Avicel®, Avicel® PH101, Avicel® PH102, Avicel® PHI05, Elcema® P100, Emcocel®, Vivacel®, Ming Tia®, and Solka-Floc®, methylcellulose, croscarmellose, or a cross-linked cellulose, such as cross-linked sodium carboxymethylcellulose (Ac-Di-Sol®), cross-linked carboxymethylcellulose, or cross-linked croscarmellose, a cross-linked starch such as sodium starch glycolate, a cross-linked polymer such as crosspovidone, a cross-linked polyvinylpyrrolidone, alginate such as alginic acid or a salt of alginic acid such as sodium alginate, a clay such as Veegum® HV (magnesium aluminum silicate), a gum such as agar, guar, locust bean, Karaya, pectin, or tragacanth, sodium starch glycolate, bentonite, a natural sponge, a surfactant, a resin such as a cation-exchange resin, citrus pulp, sodium lauryl sulfate, sodium lauryl sulfate in combination starch, and the like.

“Drug absorption” or “absorption” typically refers to the process of movement of drug from site of administration of a drug across a barrier into a blood vessel or the site of action, e.g., a drug moving from the gastrointestinal tract into the portal vein or lymphatic system.

An “enteric coating” is a substance that remains substantially intact in the stomach but dissolves and releases the drug in the small intestine or colon. Generally, the enteric coating comprises a polymeric material that prevents release in the low pH environment of the stomach but that ionizes at a higher pH, typically a pH of 6 to 7, and thus dissolves sufficiently in the small intestine or colon to release the active agent therein.

“Erosion facilitators” include materials that control the erosion of a particular material in gastrointestinal fluid. Erosion facilitators are generally known to those of ordinary skill in the art. Exemplary erosion facilitators include, e.g., hydrophilic polymers, electrolytes, proteins, peptides, and amino acids.

“Filling agents” include compounds such as lactose, calcium carbonate, calcium phosphate, dibasic calcium phosphate, calcium sulfate, microcrystalline cellulose, cellulose powder, dextrose, dextrates, dextran, starches, pregelatinized starch, sucrose, xylitol, lactitol, mannitol, sorbitol, sodium chloride, polyethylene glycol, and the like.

“Flavoring agents” and/or “sweeteners” useful in the formulations described herein, include, e.g., acacia syrup, acesulfame K, alitame, anise, apple, aspartame, banana, Bavarian cream, berry, black currant, butterscotch, calcium citrate, camphor, caramel, cherry, cherry cream, chocolate, cinnamon, bubble gum, citrus, citrus punch, citrus cream, cotton candy, cocoa, cola, cool cherry, cool citrus, cyclamate, cylamate, dextrose, eucalyptus, eugenol, fructose, fruit punch, ginger, glycyrrhetinate, glycyrrhiza (licorice) syrup, grape, grapefruit, honey, isomalt, lemon, lime, lemon cream, monoammonium glyrrhizinate (MagnaSweet®), maltol, mannitol, maple, marshmallow, menthol, mint cream, mixed berry, neohesperidine DC, neotame, orange, pear, peach, peppermint, peppermint cream, Prosweet® Powder, raspberry, root beer, rum, saccharin, safrole, sorbitol, spearmint, spearmint cream, strawberry, strawberry cream, stevia, sucralose, sucrose, sodium saccharin, saccharin, aspartame, acesulfame potassium, mannitol, talin, sylitol, sucralose, sorbitol, Swiss cream, tagatose, tangerine, thaumatin, tutti fruitti, vanilla, walnut, watermelon, wild cherry, wintergreen, xylitol, or any combination of these flavoring ingredients, e.g., anise-menthol, cherry-anise, cinnamon-orange, cherry-cinnamon, chocolate-mint, honey-lemon, lemon-lime, lemon-mint, menthol-eucalyptus, orange-cream, vanilla-mint, and mixtures thereof.

“Lubricants” and “glidants” are compounds that prevent, reduce or inhibit adhesion or friction of materials. Exemplary lubricants include, e.g., stearic acid, calcium hydroxide, talc, sodium stearyl fumerate, a hydrocarbon such as mineral oil, or hydrogenated vegetable oil such as hydrogenated soybean oil (Sterotex®), higher fatty acids and their alkali-metal and alkaline earth metal salts, such as aluminum, calcium, magnesium, zinc, stearic acid, sodium stearates, glycerol, talc, waxes, Stearowet®, boric acid, sodium benzoate, sodium acetate, sodium chloride, leucine, a polyethylene glycol (e.g., PEG-4000) or a methoxypolyethylene glycol such as Carbowax™, sodium oleate, sodium benzoate, glyceryl behenate, polyethylene glycol, magnesium or sodium lauryl sulfate, colloidal silica such as Syloid™, Cab-O—Sil®, a starch such as corn starch, silicone oil, a surfactant, and the like.

A “measurable serum concentration” or “measurable plasma concentration” describes the blood serum or blood plasma concentration, typically measured in mg, μg, or ng of therapeutic agent per ml, dl, or 1 of blood serum, absorbed into the bloodstream after administration. As used herein, measurable plasma concentrations are typically measured in ng/ml or μg/ml.

“Pharmacodynamics” refers to the factors which determine the biologic response observed relative to the concentration of drug at a site of action.

“Pharmacokinetics” refers to the factors which determine the attainment and maintenance of the appropriate concentration of drug at a site of action.

“Plasticizers” are compounds used to soften the microencapsulation material or film coatings to make them less brittle. Suitable plasticizers include, e.g., polyethylene glycols such as PEG 300, PEG 400, PEG 600, PEG 1450, PEG 3350, and PEG 800, stearic acid, propylene glycol, oleic acid, triethyl cellulose and triacetin. In some embodiments, plasticizers can also function as dispersing agents or wetting agents.

“Solubilizers” include compounds such as triacetin, triethylcitrate, ethyl oleate, ethyl caprylate, sodium lauryl sulfate, sodium doccusate, vitamin E TPGS, dimethylacetamide, N-methylpyrrolidone, N-hydroxyethylpyrrolidone, polyvinylpyrrolidone, hydroxypropylmethyl cellulose, hydroxypropyl cyclodextrins, ethanol, n-butanol, isopropyl alcohol, cholesterol, bile salts, polyethylene glycol 200-600, glycofurol, transcutol, propylene glycol, and dimethyl isosorbide and the like.

“Stabilizers” include compounds such as any antioxidation agents, buffers, acids, preservatives and the like.

“Steady state,” as used herein, is when the amount of drug administered is equal to the amount of drug eliminated within one dosing interval resulting in a plateau or constant plasma drug exposure.

“Suspending agents” include compounds such as polyvinylpyrrolidone, e.g., polyvinylpyrrolidone K12, polyvinylpyrrolidone K17, polyvinylpyrrolidone K25, or polyvinylpyrrolidone K30, vinyl pyrrolidone/vinyl acetate copolymer (S630), polyethylene glycol, e.g., the polyethylene glycol can have a molecular weight of about 300 to about 6000, or about 3350 to about 4000, or about 7000 to about 5400, sodium carboxymethylcellulose, methylcellulose, hydroxypropylmethylcellulose, hydroxymethylcellulose acetate stearate, polysorbate-80, hydroxyethylcellulose, sodium alginate, gums, such as, e.g., gum tragacanth and gum acacia, guar gum, xanthans, including xanthan gum, sugars, cellulosics, such as, e.g., sodium carboxymethylcellulose, methylcellulose, sodium carboxymethylcellulose, hydroxypropylmethylcellulose, hydroxyethylcellulose, polysorbate-80, sodium alginate, polyethoxylated sorbitan monolaurate, polyethoxylated sorbitan monolaurate, povidone and the like.

“Surfactants” include compounds such as sodium lauryl sulfate, sodium docusate, Tween 60 or 80, triacetin, vitamin E TPGS, sorbitan monooleate, polyoxyethylene sorbitan monooleate, polysorbates, polaxomers, bile salts, glyceryl monostearate, copolymers of ethylene oxide and propylene oxide, e.g., Pluronic® (BASF), and the like. Some other surfactants include polyoxyethylene fatty acid glycerides and vegetable oils, e.g., polyoxyethylene (60) hydrogenated castor oil; and polyoxyethylene alkyl ethers and alkylphenyl ethers, e.g., octoxynol 10, octoxynol 40. In some embodiments, surfactants may be included to enhance physical stability or for other purposes.

“Viscosity enhancing agents” include, e.g., methyl cellulose, xanthan gum, carboxymethyl cellulose, hydroxypropyl cellulose, hydroxypropylmethyl cellulose, hydroxypropylmethyl cellulose acetate stearate, hydroxypropylmethyl cellulose phthalate, carbomer, polyvinyl alcohol, alginates, acacia, chitosans and combinations thereof.

“Wetting agents” include compounds such as oleic acid, glyceryl monostearate, sorbitan monooleate, sorbitan monolaurate, triethanolamine oleate, polyoxyethylene sorbitan monooleate, polyoxyethylene sorbitan monolaurate, sodium docusate, sodium oleate, sodium lauryl sulfate, sodium doccusate, triacetin, Tween 80, vitamin E TPGS, ammonium salts and the like.

Dosage Forms

The compositions described herein can be formulated for administration to a subject via any conventional means including, but not limited to, oral, parenteral (e.g., intravenous, subcutaneous, or intramuscular), buccal, intranasal, rectal or transdermal administration routes. As used herein, the term “subject” is used to mean an animal, preferably a mammal, including a human or non-human. The terms patient and subject may be used interchangeably.

Moreover, the pharmaceutical compositions described herein, which include a compound of any of Formula (I)-(XXIIIh) can be formulated into any suitable dosage form, including but not limited to, aqueous oral dispersions, liquids, gels, syrups, elixirs, slurries, suspensions and the like, for oral ingestion by a patient to be treated, solid oral dosage forms, aerosols, controlled release formulations, fast melt formulations, effervescent formulations, lyophilized formulations, tablets, powders, pills, dragees, capsules, delayed release formulations, extended release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate release and controlled release formulations.

Pharmaceutical preparations for oral use can be obtained by mixing one or more solid excipient with one or more of the compounds described herein, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients include, for example, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, sodium carboxymethylcellulose; or others such as: polyvinylpyrrolidone (PVP or povidone) or calcium phosphate. If desired, disintegrating agents may be added, such as the cross-linked croscarmellose sodium, polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for such administration.

In some embodiments, the solid dosage forms disclosed herein may be in the form of a tablet, (including a suspension tablet, a fast-melt tablet, a bite-disintegration tablet, a rapid-disintegration tablet, an effervescent tablet, or a caplet), a pill, a powder (including a sterile packaged powder, a dispensable powder, or an effervescent powder) a capsule (including both soft or hard capsules, e.g., capsules made from animal-derived gelatin or plant-derived HPMC, or “sprinkle capsules”), solid dispersion, solid solution, bioerodible dosage form, controlled release formulations, pulsatile release dosage forms, multiparticulate dosage forms, pellets, granules, or an aerosol. In some embodiments, the pharmaceutical composition is in the form of a powder. In some embodiments, the pharmaceutical composition is in the form of a tablet, including but not limited to, a fast-melt tablet. Additionally, pharmaceutical compositions described herein may be administered as a single capsule or in multiple capsule dosage form. In some embodiments, the pharmaceutical composition is administered in two, or three, or four, capsules or tablets.

In some embodiments, solid dosage forms, e.g., tablets, effervescent tablets, and capsules, are prepared by mixing particles of a compound of any of Formula (I)-(XXIIIh) with one or more pharmaceutical excipients to form a bulk blend composition. When referring to these bulk blend compositions as homogeneous, it is meant that the particles of the compound of any of Formula (I)-(XXIIIh) are dispersed evenly throughout the composition so that the composition may be readily subdivided into equally effective unit dosage forms, such as tablets, pills, and capsules. The individual unit dosages may also include film coatings, which disintegrate upon oral ingestion or upon contact with diluent. These formulations can be manufactured by conventional pharmacological techniques.

Conventional pharmacological techniques include, e.g., one or a combination of methods: (1) dry mixing, (2) direct compression, (3) milling, (4) dry or non-aqueous granulation, (5) wet granulation, or (6) fusion. See, e.g., Lachman et al., The Theory and Practice of Industrial Pharmacy (1986). Other methods include, e.g., spray drying, pan coating, melt granulation, granulation, fluidized bed spray drying or coating (e.g., wurster coating), tangential coating, top spraying, tableting, extruding and the like.

The pharmaceutical solid dosage forms described herein can include a compound described herein and one or more pharmaceutically acceptable additives such as a compatible carrier, binder, filling agent, suspending agent, flavoring agent, sweetening agent, disintegrating agent, dispersing agent, surfactant, lubricant, colorant, diluent, solubilizer, moistening agent, plasticizer, stabilizer, penetration enhancer, wetting agent, anti-foaming agent, antioxidant, preservative, or one or more combination thereof. In some embodiments, using standard coating procedures, such as those described in Remington's Pharmaceutical Sciences, 20th Edition (2000), a film coating is provided around the formulation of the compound of any of Formula (I)-(XXIIIh). In some embodiments, some or all of the particles of the compound of any of Formula (I)-(XXIIIh) are coated. In some embodiments, some or all of the particles of the compound of any of Formula (I)-(XXIIIh), are microencapsulated. In still some embodiments, the particles of the compound of any of Formula (I)-(XXIIIh) are not microencapsulated and are uncoated.

Suitable carriers for use in the solid dosage forms described herein include, but are not limited to, acacia, gelatin, colloidal silicon dioxide, calcium glycerophosphate, calcium lactate, maltodextrin, glycerine, magnesium silicate, sodium caseinate, soy lecithin, sodium chloride, tricalcium phosphate, dipotassium phosphate, sodium stearoyl lactylate, carrageenan, monoglyceride, diglyceride, pregelatinized starch, hydroxypropylmethylcellulose, hydroxypropylmethylcellulose acetate stearate, sucrose, microcrystalline cellulose, lactose, mannitol and the like.

Suitable filling agents for use in the solid dosage forms described herein include, but are not limited to, lactose, calcium carbonate, calcium phosphate, dibasic calcium phosphate, calcium sulfate, microcrystalline cellulose, cellulose powder, dextrose, dextrates, dextran, starches, pregelatinized starch, hydroxypropylmethycellulose (HPMC), hydroxypropylmethycellulose phthalate, hydroxypropylmethylcellulose acetate stearate (HPMCAS), sucrose, xylitol, lactitol, mannitol, sorbitol, sodium chloride, polyethylene glycol, and the like.

In order to release the compound of any of Formula (I)-(XXIIIh) from a solid dosage form matrix as efficiently as possible, disintegrants are often used in the formulation, especially when the dosage forms are compressed with binder. Disintegrants help rupturing the dosage form matrix by swelling or capillary action when moisture is absorbed into the dosage form. Suitable disintegrants for use in the solid dosage forms described herein include, but are not limited to, natural starch such as corn starch or potato starch, a pregelatinized starch such as National 1551 or Amijel®, or sodium starch glycolate such as Promogel® or Explotab®, a cellulose such as a wood product, methyl crystalline cellulose, e.g., Avicel®, Avicel® PH101, Avicel® PH102, Avicel® PHI05, Elcema® P100, Emcocel®, Vivacel®, Ming Tia®, and Solka-Floc®, methylcellulose, croscarmellose, or a cross-linked cellulose, such as cross-linked sodium carboxymethylcellulose (Ac-Di-Sol®), cross-linked carboxymethylcellulose, or cross-linked croscarmellose, a cross-linked starch such as sodium starch glycolate, a cross-linked polymer such as crospovidone, a cross-linked polyvinylpyrrolidone, alginate such as alginic acid or a salt of alginic acid such as sodium alginate, a clay such as Veegum® HV (magnesium aluminum silicate), a gum such as agar, guar, locust bean, Karaya, pectin, or tragacanth, sodium starch glycolate, bentonite, a natural sponge, a surfactant, a resin such as a cation-exchange resin, citrus pulp, sodium lauryl sulfate, sodium lauryl sulfate in combination starch, and the like.

Binders impart cohesiveness to solid oral dosage form formulations: for powder filled capsule formulation, they aid in plug formation that can be filled into soft or hard shell capsules and for tablet formulation, they ensure the tablet remaining intact after compression and help assure blend uniformity prior to a compression or fill step. Materials suitable for use as binders in the solid dosage forms described herein include, but are not limited to, carboxymethylcellulose, methylcellulose (e.g., Methocel®), hydroxypropylmethylcellulose (e.g. Hypromellose USP Pharmacoat-603, hydroxypropylmethylcellulose acetate stearate (Aqoate HS-LF and HS), hydroxyethylcellulose, hydroxypropylcellulose (e.g., Klucel®), ethylcellulose (e.g., Ethocel®), and microcrystalline cellulose (e.g., Avicel®), microcrystalline dextrose, amylose, magnesium aluminum silicate, polysaccharide acids, bentonites, gelatin, polyvinylpyrrolidone/vinyl acetate copolymer, crospovidone, povidone, starch, pregelatinized starch, tragacanth, dextrin, a sugar, such as sucrose (e.g., Dipac®), glucose, dextrose, molasses, mannitol, sorbitol, xylitol (e.g., Xylitab®), lactose, a natural or synthetic gum such as acacia, tragacanth, ghatti gum, mucilage of isapol husks, starch, polyvinylpyrrolidone (e.g., Povidone® CL, Kollidon® CL, Polyplasdone® XL-10, and Povidone® K-12), larch arabogalactan, Veegum®, polyethylene glycol, waxes, sodium alginate, and the like.

In general, binder levels of 20-70% are used in powder-filled gelatin capsule formulations. Binder usage level in tablet formulations varies whether direct compression, wet granulation, roller compaction, or usage of other excipients such as fillers which itself can act as moderate binder. Formulators skilled in art can determine the binder level for the formulations, but binder usage level of up to 70% in tablet formulations is common.

Suitable lubricants or glidants for use in the solid dosage forms described herein include, but are not limited to, stearic acid, calcium hydroxide, talc, corn starch, sodium stearyl fumerate, alkali-metal and alkaline earth metal salts, such as aluminum, calcium, magnesium, zinc, stearic acid, sodium stearates, magnesium stearate, zinc stearate, waxes, Stearowet®, boric acid, sodium benzoate, sodium acetate, sodium chloride, leucine, a polyethylene glycol or a methoxypolyethylene glycol such as Carbowax™, PEG 4000, PEG 5000, PEG 6000, propylene glycol, sodium oleate, glyceryl behenate, glyceryl palmitostearate, glyceryl benzoate, magnesium or sodium lauryl sulfate, and the like.

Suitable diluents for use in the solid dosage forms described herein include, but are not limited to, sugars (including lactose, sucrose, and dextrose), polysaccharides (including dextrates and maltodextrin), polyols (including mannitol, xylitol, and sorbitol), cyclodextrins and the like.

The term “non water-soluble diluent” represents compounds typically used in the formulation of pharmaceuticals, such as calcium phosphate, calcium sulfate, starches, modified starches and microcrystalline cellulose, and microcellulose (e.g., having a density of about 0.45 g/cm³, e.g. Avicel, powdered cellulose), and talc.

Suitable wetting agents for use in the solid dosage forms described herein include, for example, oleic acid, glyceryl monostearate, sorbitan monooleate, sorbitan monolaurate, triethanolamine oleate, polyoxyethylene sorbitan monooleate, polyoxyethylene sorbitan monolaurate, quaternary ammonium compounds (e.g., Polyquat 10®), sodium oleate, sodium lauryl sulfate, magnesium stearate, sodium docusate, triacetin, vitamin E TPGS and the like.

Suitable surfactants for use in the solid dosage forms described herein include, for example, sodium lauryl sulfate, sorbitan monooleate, polyoxyethylene sorbitan monooleate, polysorbates, polaxomers, bile salts, glyceryl monostearate, copolymers of ethylene oxide and propylene oxide, e.g., Pluronic® (BASF), and the like.

Suitable suspending agents for use in the solid dosage forms described here include, but are not limited to, polyvinylpyrrolidone, e.g., polyvinylpyrrolidone K12, polyvinylpyrrolidone K17, polyvinylpyrrolidone K25, or polyvinylpyrrolidone K30, polyethylene glycol, e.g., the polyethylene glycol can have a molecular weight of about 300 to about 6000, or about 3350 to about 4000, or about 7000 to about 5400, vinyl pyrrolidone/vinyl acetate copolymer (S630), sodium carboxymethylcellulose, methyl cellulose, hydroxy-propylmethylcellulose, polysorbate-80, hydroxyethylcellulose, sodium alginate, gums, such as, e.g., gum tragacanth and gum acacia, guar gum, xanthans, including xanthan gum, sugars, cellulosics, such as, e.g., sodium carboxymethylcellulose, methylcellulose, sodium carboxymethylcellulose, hydroxypropylmethylcellulose, hydroxyethylcellulose, polysorbate-80, sodium alginate, polyethoxylated sorbitan monolaurate, polyethoxylated sorbitan monolaurate, povidone and the like.

Suitable antioxidants for use in the solid dosage forms described herein include, for example, e.g., butylated hydroxytoluene (BHT), sodium ascorbate, and tocopherol.

It should be appreciated that there is considerable overlap between additives used in the solid dosage forms described herein. Thus, the above-listed additives should be taken as merely exemplary, and not limiting, of the types of additives that can be included in solid dosage forms described herein. The amounts of such additives can be readily determined by one skilled in the art, according to the particular properties desired.

In some embodiments, one or more layers of the pharmaceutical composition are plasticized. Illustratively, a plasticizer is generally a high boiling point solid or liquid. Suitable plasticizers can be added from about 0.01% to about 50% by weight (w/w) of the coating composition. Plasticizers include, but are not limited to, diethyl phthalate, citrate esters, polyethylene glycol, glycerol, acetylated glycerides, triacetin, polypropylene glycol, polyethylene glycol, triethyl citrate, dibutyl sebacate, stearic acid, stearol, stearate, and castor oil.

Compressed tablets are solid dosage forms prepared by compacting the bulk blend of the formulations described above. In various embodiments, compressed tablets which are designed to dissolve in the mouth will include one or more flavoring agents. In some embodiments, the compressed tablets will include a film surrounding the final compressed tablet. In some embodiments, the film coating can provide a delayed release of the compound of of any of Formula (I)-(XXIIIh) from the formulation. In some embodiments, the film coating aids in patient compliance (e.g., Opadry® coatings or sugar coating). Film coatings including Opadry® typically range from about 1% to about 3% of the tablet weight. In some embodiments, the compressed tablets include one or more excipients.

A capsule may be prepared, for example, by placing the bulk blend of the formulation of the compound of any of Formula (I)-(XXIIIh), described above, inside of a capsule. In some embodiments, the formulations (non-aqueous suspensions and solutions) are placed in a soft gelatin capsule. In some embodiments, the formulations are placed in standard gelatin capsules or non-gelatin capsules such as capsules comprising HPMC. In some embodiments, the formulation is placed in a sprinkle capsule, wherein the capsule may be swallowed whole or the capsule may be opened and the contents sprinkled on food prior to eating. In some embodiments, the therapeutic dose is split into multiple (e.g., two, three, or four) capsules. In some embodiments, the entire dose of the formulation is delivered in a capsule form.

In various embodiments, the particles of the compound of any of Formula (I)-(XXIIIh) and one or more excipients are dry blended and compressed into a mass, such as a tablet, having a hardness sufficient to provide a pharmaceutical composition that substantially disintegrates within less than about 30 minutes, less than about 35 minutes, less than about 40 minutes, less than about 45 minutes, less than about 50 minutes, less than about 55 minutes, or less than about 60 minutes, after oral administration, thereby releasing the formulation into the gastrointestinal fluid.

In some embodiments, dosage forms may include microencapsulated formulations. In some embodiments, one or more other compatible materials are present in the microencapsulation material. Exemplary materials include, but are not limited to, pH modifiers, erosion facilitators, anti-foaming agents, antioxidants, flavoring agents, and carrier materials such as binders, suspending agents, disintegration agents, filling agents, surfactants, solubilizers, stabilizers, lubricants, wetting agents, and diluents.

Materials useful for the microencapsulation described herein include materials compatible with compounds of any of Formula (I)-(XXIIIh) which sufficiently isolate the compound of any of Formula (I)-(XXIIIh) from other non-compatible excipients. Materials compatible with compounds of any of Formula (I)-(XXIIIh) are those that delay the release of the compounds of any of Formula (I)-(XXIIIh), in vivo.

Exemplary microencapsulation materials useful for delaying the release of the formulations including compounds described herein, include, but are not limited to, hydroxypropyl cellulose ethers (HPC) such as Klucel® or Nisso HPC, low-substituted hydroxypropyl cellulose ethers (L-HPC), hydroxypropyl methyl cellulose ethers (HPMC) such as Seppifilm-LC, Pharmacoat®, Metolose SR, Methocel®-E, Opadry YS, PrimaFlo, Benecel MP824, and Benecel MP843, methylcellulose polymers such as Methocel®-A, hydroxypropylmethylcellulose acetate stearate Aqoat (HF-LS, HF-LG, HF-MS) and Metolose®, Ethylcelluloses (EC) and mixtures thereof such as E461, Ethocel®, Aqualon®-EC, Surelease®, Polyvinyl alcohol (PVA) such as Opadry AMB, hydroxyethylcelluloses such as Natrosol®, carboxymethylcelluloses and salts of carboxymethylcelluloses (CMC) such as Aqualon®-CMC, polyvinyl alcohol and polyethylene glycol co-polymers such as Kollicoat IR®, monoglycerides (Myverol), triglycerides (KLX), polyethylene glycols, modified food starch, acrylic polymers and mixtures of acrylic polymers with cellulose ethers such as Eudragit® EPO, Eudragit® L30D-55, Eudragit® FS 30D Eudragit® L100-55, Eudragit® L100, Eudragit® S100, Eudragit® RD100, Eudragit® E100, Eudragit® L12.5, Eudragit® S12.5, Eudragit® NE30D, and Eudragit® NE 40D, cellulose acetate phthalate, sepifilms such as mixtures of HPMC and stearic acid, cyclodextrins, and mixtures of these materials.

In some embodiments, plasticizers such as polyethylene glycols, e.g., PEG 300, PEG 400, PEG 600, PEG 1450, PEG 3350, and PEG 800, stearic acid, propylene glycol, oleic acid, and triacetin are incorporated into the microencapsulation material. In some embodiments, the microencapsulating material useful for delaying the release of the pharmaceutical compositions is from the USP or the National Formulary (NF). In some embodiments, the microencapsulation material is Klucel. In some embodiments, the microencapsulation material is methocel.

Microencapsulated compounds of any of Formula (I)-(XXIIIh) may be formulated by methods known by one of ordinary skill in the art. Such known methods include, e.g., spray drying processes, spinning disk-solvent processes, hot melt processes, spray chilling methods, fluidized bed, electrostatic deposition, centrifugal extrusion, rotational suspension separation, polymerization at liquid-gas or solid-gas interface, pressure extrusion, or spraying solvent extraction bath. In addition to these, several chemical techniques, e.g., complex coacervation, solvent evaporation, polymer-polymer incompatibility, interfacial polymerization in liquid media, in situ polymerization, in-liquid drying, and desolvation in liquid media could also be used. Furthermore, other methods such as roller compaction, extrusion/spheronization, coacervation, or nanoparticle coating may also be used.

In some embodiments, the particles of compounds of any of Formula (I)-(XXIIIh) are microencapsulated prior to being formulated into one of the above forms. In still some embodiments, some or most of the particles are coated prior to being further formulated by using standard coating procedures, such as those described in Remington's Pharmaceutical Sciences, 20th Edition (2000).

In some embodiments, the solid dosage formulations of the compounds of any of Formula (I)-(XXIIIh) are plasticized (coated) with one or more layers. Illustratively, a plasticizer is generally a high boiling point solid or liquid. Suitable plasticizers can be added from about 0.01% to about 50% by weight (w/w) of the coating composition. Plasticizers include, but are not limited to, diethyl phthalate, citrate esters, polyethylene glycol, glycerol, acetylated glycerides, triacetin, polypropylene glycol, polyethylene glycol, triethyl citrate, dibutyl sebacate, stearic acid, stearol, stearate, and castor oil.

In some embodiments, a powder including the formulations with a compound of any of Formula (I)-(XXIIIh), described herein, may be formulated to include one or more pharmaceutical excipients and flavors. Such a powder may be prepared, for example, by mixing the formulation and optional pharmaceutical excipients to form a bulk blend composition. Additional embodiments also include a suspending agent and/or a wetting agent. This bulk blend is uniformly subdivided into unit dosage packaging or multi-dosage packaging units.

In still some embodiments, effervescent powders are also prepared in accordance with the present disclosure. Effervescent salts have been used to disperse medicines in water for oral administration. Effervescent salts are granules or coarse powders containing a medicinal agent in a dry mixture, usually composed of sodium bicarbonate, citric acid and/or tartaric acid. When salts of the compositions described herein are added to water, the acids and the base react to liberate carbon dioxide gas, thereby causing “effervescence.” Examples of effervescent salts include, e.g., the following ingredients: sodium bicarbonate or a mixture of sodium bicarbonate and sodium carbonate, citric acid and/or tartaric acid. Any acid-base combination that results in the liberation of carbon dioxide can be used in place of the combination of sodium bicarbonate and citric and tartaric acids, as long as the ingredients were suitable for pharmaceutical use and result in a pH of about 6.0 or higher.

In some embodiments, the formulations described herein, which include a compound of Formula (A), are solid dispersions. Methods of producing such solid dispersions are known in the art and include, but are not limited to, for example, U.S. Pat. Nos. 4,343,789, 5,340,591, 5,456,923, 5,700,485, 5,723,269, and U.S. Pub. Appl 2004/0013734, each of which is specifically incorporated by reference. In some embodiments, the formulations described herein are solid solutions. Solid solutions incorporate a substance together with the active agent and other excipients such that heating the mixture results in dissolution of the drug and the resulting composition is then cooled to provide a solid blend which can be further formulated or directly added to a capsule or compressed into a tablet. Methods of producing such solid solutions are known in the art and include, but are not limited to, for example, U.S. Pat. Nos. 4,151,273, 5,281,420, and 6,083,518, each of which is specifically incorporated by reference.

The pharmaceutical solid oral dosage forms including formulations described herein, which include a compound of any of Formula (I)-(XXIIIh) can be further formulated to provide a controlled release of the compound of Formula (A). Controlled release refers to the release of the compound of any of Formula (I)-(XXIIIh) from a dosage form in which it is incorporated according to a desired profile over an extended period of time. Controlled release profiles include, for example, sustained release, prolonged release, pulsatile release, and delayed release profiles. In contrast to immediate release compositions, controlled release compositions allow delivery of an agent to a subject over an extended period of time according to a predetermined profile. Such release rates can provide therapeutically effective levels of agent for an extended period of time and thereby provide a longer period of pharmacologic response while minimizing side effects as compared to conventional rapid release dosage forms. Such longer periods of response provide for many inherent benefits that are not achieved with the corresponding short acting, immediate release preparations.

In some embodiments, the solid dosage forms described herein can be formulated as enteric coated delayed release oral dosage forms, i.e., as an oral dosage form of a pharmaceutical composition as described herein which utilizes an enteric coating to affect release in the small intestine of the gastrointestinal tract. The enteric coated dosage form may be a compressed or molded or extruded tablet/mold (coated or uncoated) containing granules, powder, pellets, beads or particles of the active ingredient and/or other composition components, which are themselves coated or uncoated. The enteric coated oral dosage form may also be a capsule (coated or uncoated) containing pellets, beads or granules of the solid carrier or the composition, which are themselves coated or uncoated.

The term “delayed release” as used herein refers to the delivery so that the release can be accomplished at some generally predictable location in the intestinal tract more distal to that which would have been accomplished if there had been no delayed release alterations. In some embodiments the method for delay of release is coating. Any coatings should be applied to a sufficient thickness such that the entire coating does not dissolve in the gastrointestinal fluids at pH below about 5, but does dissolve at pH about 5 and above. It is expected that any anionic polymer exhibiting a pH-dependent solubility profile can be used as an enteric coating in the methods and compositions described herein to achieve delivery to the lower gastrointestinal tract. In some embodiments the polymers described herein are anionic carboxylic polymers. In some embodiments, the polymers and compatible mixtures thereof, and some of their properties, include, but are not limited to:

Shellac, also called purified lac, a refined product obtained from the resinous secretion of an insect. This coating dissolves in media of pH>7;

Acrylic polymers. The performance of acrylic polymers (primarily their solubility in biological fluids) can vary based on the degree and type of substitution. Examples of suitable acrylic polymers include methacrylic acid copolymers and ammonium methacrylate copolymers. The Eudragit series E, L, S, RL, RS and NE (Rohm Pharma) are available as solubilized in organic solvent, aqueous dispersion, or dry powders. The Eudragit series RL, NE, and RS are insoluble in the gastrointestinal tract but are permeable and are used primarily for colonic targeting. The Eudragit series E dissolve in the stomach. The Eudragit series L, L-30D and S are insoluble in stomach and dissolve in the intestine.

Cellulose Derivatives. Examples of suitable cellulose derivatives are: ethyl cellulose; reaction mixtures of partial acetate esters of cellulose with phthalic anhydride. The performance can vary based on the degree and type of substitution. Cellulose acetate phthalate (CAP) dissolves in pH>6. Aquateric (FMC) is an aqueous based system and is a spray dried CAP psuedolatex with particles <1 μm. Other components in Aquateric can include pluronics, Tweens, and acetylated monoglycerides. Other suitable cellulose derivatives include: cellulose acetate trimellitate (Eastman); methylcellulose (Pharmacoat, Methocel); hydroxypropylmethyl cellulose phthalate (HPMCP); hydroxypropylmethyl cellulose succinate (HPMCS); and hydroxypropylmethylcellulose acetate succinate (e.g., AQOAT (Shin Etsu)). The performance can vary based on the degree and type of substitution. For example, HPMCP such as, HP-50, HP-55, HP-55S, HP-55F grades are suitable. The performance can vary based on the degree and type of substitution. For example, suitable grades of hydroxypropylmethylcellulose acetate succinate include, but are not limited to, AS-LG (LF), which dissolves at pH 5, AS-MG (MF), which dissolves at pH 5.5, and AS-HG (HF), which dissolves at higher pH. These polymers are offered as granules, or as fine powders for aqueous dispersions;

Poly Vinyl Acetate Phthalate (PVAP). PVAP dissolves in pH>5, and it is much less permeable to water vapor and gastric fluids.

In some embodiments, the coating can, and usually does, contain a plasticizer and possibly other coating excipients such as colorants, talc, and/or magnesium stearate, which are well known in the art. Suitable plasticizers include triethyl citrate (Citroflex 2), triacetin (glyceryl triacetate), acetyl triethyl citrate (Citroflec A2), Carbowax 400 (polyethylene glycol 400), diethyl phthalate, tributyl citrate, acetylated monoglycerides, glycerol, fatty acid esters, propylene glycol, and dibutyl phthalate. In particular, anionic carboxylic acrylic polymers usually will contain 10-25% by weight of a plasticizer, especially dibutyl phthalate, polyethylene glycol, triethyl citrate and triacetin. Conventional coating techniques such as spray or pan coating are employed to apply coatings. The coating thickness must be sufficient to ensure that the oral dosage form remains intact until the desired site of topical delivery in the intestinal tract is reached.

Colorants, detackifiers, surfactants, antifoaming agents, lubricants (e.g., carnuba wax or PEG) may be added to the coatings besides plasticizers to solubilize or disperse the coating material, and to improve coating performance and the coated product.

In some embodiments, the formulations described herein, which include a compound of Formula (A), are delivered using a pulsatile dosage form. A pulsatile dosage form is capable of providing one or more immediate release pulses at predetermined time points after a controlled lag time or at specific sites. Pulsatile dosage forms including the formulations described herein, which include a compound of any of Formula (I)-(XXIIIh) may be administered using a variety of pulsatile formulations known in the art. For example, such formulations include, but are not limited to, those described in U.S. Pat. Nos. 5,011,692, 5,017,381, 5,229,135, and 5,840,329, each of which is specifically incorporated by reference. Other pulsatile release dosage forms suitable for use with the present formulations include, but are not limited to, for example, U.S. Pat. Nos. 4,871,549, 5,260,068, 5,260,069, 5,508,040, 5,567,441 and 5,837,284, all of which are specifically incorporated by reference. In some embodiments, the controlled release dosage form is pulsatile release solid oral dosage form including at least two groups of particles, (i.e. multiparticulate) each containing the formulation described herein. The first group of particles provides a substantially immediate dose of the compound of any of Formula (I)-(XXIIIh) upon ingestion by a mammal. The first group of particles can be either uncoated or include a coating and/or sealant. The second group of particles includes coated particles, which includes from about 2% to about 75%, from about 2.5% to about 70%, or from about 40% to about 70%, by weight of the total dose of the compound of any of Formula (I)-(XXIIIh) in said formulation, in admixture with one or more binders. The coating includes a pharmaceutically acceptable ingredient in an amount sufficient to provide a delay of from about 2 hours to about 7 hours following ingestion before release of the second dose. Suitable coatings include one or more differentially degradable coatings such as, by way of example only, pH sensitive coatings (enteric coatings) such as acrylic resins (e.g., Eudragit® EPO, Eudragit® L30D-55, Eudragit® FS 30D Eudragit® L100-55, Eudragit® L100, Eudragit® S100, Eudragit® RD100, Eudragit® E100, Eudragit® L12.5, Eudragit® S12.5, and Eudragit® NE30D, Eudragit® NE 40D®) either alone or blended with cellulose derivatives, e.g., ethylcellulose, or non-enteric coatings having variable thickness to provide differential release of the formulation that includes a compound of any of Formula (I).

Many other types of controlled release systems known to those of ordinary skill in the art and are suitable for use with the formulations described herein. Examples of such delivery systems include, e.g., polymer-based systems, such as polylactic and polyglycolic acid, polyanhydrides and polycaprolactone; porous matrices, nonpolymer-based systems that are lipids, including sterols, such as cholesterol, cholesterol esters and fatty acids, or neutral fats, such as mono-, di- and triglycerides; hydrogel release systems; silastic systems; peptide-based systems; wax coatings, bioerodible dosage forms, compressed tablets using conventional binders and the like. See, e.g., Liberman et al., Pharmaceutical Dosage Forms, 2 Ed., Vol. 1, pp. 209-214 (1990); Singh et al., Encyclopedia of Pharmaceutical Technology, 2^(nd) Ed., pp. 751-753 (2002); U.S. Pat. Nos. 4,327,725, 4,624,848, 4,968,509, 5,461,140, 5,456,923, 5,516,527, 5,622,721, 5,686,105, 5,700,410, 5,977,175, 6,465,014 and 6,932,983, each of which is specifically incorporated by reference.

In some embodiments, pharmaceutical compositions are provided that include particles of the compounds of any of Formula (I)-(XXIIIh), described herein and at least one dispersing agent or suspending agent for oral administration to a subject. The formulations may be a powder and/or granules for suspension, and upon admixture with water, a substantially uniform suspension is obtained.

Liquid formulation dosage forms for oral administration can be aqueous suspensions selected from the group including, but not limited to, pharmaceutically acceptable aqueous oral dispersions, emulsions, solutions, elixirs, gels, and syrups. See, e.g., Singh et al., Encyclopedia of Pharmaceutical Technology, 2^(nd) Ed., pp. 754-757 (2002). In addition to the particles of compound of Formula (A), the liquid dosage forms may include additives, such as: (a) disintegrating agents; (b) dispersing agents; (c) wetting agents; (d) at least one preservative, (e) viscosity enhancing agents, (f) at least one sweetening agent, and (g) at least one flavoring agent. In some embodiments, the aqueous dispersions can further include a crystalline inhibitor.

The aqueous suspensions and dispersions described herein can remain in a homogenous state, as defined in The USP Pharmacists' Pharmacopeia (2005 edition, chapter 905), for at least 4 hours. The homogeneity should be determined by a sampling method consistent with regard to determining homogeneity of the entire composition. In some embodiments, an aqueous suspension can be re-suspended into a homogenous suspension by physical agitation lasting less than 1 minute. In some embodiments, an aqueous suspension can be re-suspended into a homogenous suspension by physical agitation lasting less than 45 seconds. In yet some embodiments, an aqueous suspension can be re-suspended into a homogenous suspension by physical agitation lasting less than 30 seconds. In still some embodiments, no agitation is necessary to maintain a homogeneous aqueous dispersion.

Examples of disintegrating agents for use in the aqueous suspensions and dispersions include, but are not limited to, a starch, e.g., a natural starch such as corn starch or potato starch, a pregelatinized starch such as National 1551 or Amijel®, or sodium starch glycolate such as Promogel® or Explotab®; a cellulose such as a wood product, methylcrystalline cellulose, e.g., Avicel®, Avicel® PH101, Avicel® PH102, Avicel® PH105, Elcema® P100, Emcocel®, Vivacel®, Ming Tia®, and Solka-Floc®, methylcellulose, croscarmellose, or a cross-linked cellulose, such as cross-linked sodium carboxymethylcellulose (Ac-Di-Sol®), cross-linked carboxymethylcellulose, or cross-linked croscarmellose; a cross-linked starch such as sodium starch glycolate; a cross-linked polymer such as crospovidone; a cross-linked polyvinylpyrrolidone; alginate such as alginic acid or a salt of alginic acid such as sodium alginate; a clay such as Veegum® HV (magnesium aluminum silicate); a gum such as agar, guar, locust bean, Karaya, pectin, or tragacanth; sodium starch glycolate; bentonite; a natural sponge; a surfactant; a resin such as a cation-exchange resin; citrus pulp; sodium lauryl sulfate; sodium lauryl sulfate in combination starch; and the like.

In some embodiments, the dispersing agents suitable for the aqueous suspensions and dispersions described herein are known in the art and include, for example, hydrophilic polymers, electrolytes, Tween® 60 or 80, PEG, polyvinylpyrrolidone (PVP; commercially known as Plasdone®), and the carbohydrate-based dispersing agents such as, for example, hydroxypropylcellulose and hydroxypropyl cellulose ethers (e.g., HPC, HPC-SL, and HPC-L), hydroxypropyl methylcellulose and hydroxypropyl methylcellulose ethers (e.g. HPMC K100, HPMC K4M, HPMC K15M, and HPMC K100M), carboxymethylcellulose sodium, methylcellulose, hydroxyethylcellulose, hydroxypropylmethyl-cellulose phthalate, hydroxypropylmethyl-cellulose acetate stearate, noncrystalline cellulose, magnesium aluminum silicate, triethanolamine, polyvinyl alcohol (PVA), polyvinylpyrrolidone/vinyl acetate copolymer (Plasdone®, e.g., S-630), 4-(1,1,3,3-tetramethylbutyl)-phenol polymer with ethylene oxide and formaldehyde (also known as tyloxapol), poloxamers (e.g., Pluronics F68®, F88®, and F108®, which are block copolymers of ethylene oxide and propylene oxide); and poloxamines (e.g., Tetronic 908®, also known as Poloxamine 908®, which is a tetrafunctional block copolymer derived from sequential addition of propylene oxide and ethylene oxide to ethylenediamine (BASF Corporation, Parsippany, N.J.)). In some embodiments, the dispersing agent is selected from a group not comprising one of the following agents: hydrophilic polymers; electrolytes; Tween® 60 or 80; PEG; polyvinylpyrrolidone (PVP); hydroxypropylcellulose and hydroxypropyl cellulose ethers (e.g., HPC, HPC-SL, and HPC-L); hydroxypropyl methylcellulose and hydroxypropyl methyl cellulose ethers (e.g. HPMC K100, HPMC K4M, HPMC K15M, HPMC K100M, and Pharmacoat® USP 2910 (Shin-Etsu)); carboxymethylcellulose sodium; methylcellulose; hydroxy ethyl cellulose; hydroxypropylmethyl-cellulose phthalate; hydroxypropylmethyl-cellulose acetate stearate; non-crystalline cellulose; magnesium aluminum silicate; triethanolamine; polyvinyl alcohol (PVA); 4-(1,1,3,3-tetramethylbutyl)-phenol polymer with ethylene oxide and formaldehyde; poloxamers (e.g., Pluronics F68®, F88®, and F108®, which are block copolymers of ethylene oxide and propylene oxide); or poloxamines (e.g., Tetronic 908®, also known as Poloxamine 908®).

Wetting agents suitable for the aqueous suspensions and dispersions described herein are known in the art and include, but are not limited to, cetyl alcohol, glycerol monostearate, polyoxyethylene sorbitan fatty acid esters (e.g., the commercially available Tweens® such as e.g., Tween 20® and Tween 80® (ICI Specialty Chemicals)), and polyethylene glycols (e.g., Carbowaxs 3350® and 1450®, and Carbopol 934® (Union Carbide)), oleic acid, glyceryl monostearate, sorbitan monooleate, sorbitan monolaurate, triethanolamine oleate, polyoxyethylene sorbitan monooleate, polyoxyethylene sorbitan monolaurate, sodium oleate, sodium lauryl sulfate, sodium docusate, triacetin, vitamin E TPGS, sodium taurocholate, simethicone, phosphotidylcholine and the like

Suitable preservatives for the aqueous suspensions or dispersions described herein include, for example, potassium sorbate, parabens (e.g., methylparaben and propylparaben), benzoic acid and its salts, other esters of parahydroxybenzoic acid such as butylparaben, alcohols such as ethyl alcohol or benzyl alcohol, phenolic compounds such as phenol, or quaternary compounds such as benzalkonium chloride. Preservatives, as used herein, are incorporated into the dosage form at a concentration sufficient to inhibit microbial growth.

Suitable viscosity enhancing agents for the aqueous suspensions or dispersions described herein include, but are not limited to, methyl cellulose, xanthan gum, carboxymethyl cellulose, hydroxypropyl cellulose, hydroxypropylmethyl cellulose, Plasdon® S-630, carbomer, polyvinyl alcohol, alginates, acacia, chitosans and combinations thereof. The concentration of the viscosity enhancing agent will depend upon the agent selected and the viscosity desired.

Examples of sweetening agents suitable for the aqueous suspensions or dispersions described herein include, for example, acacia syrup, acesulfame K, alitame, anise, apple, aspartame, banana, Bavarian cream, berry, black currant, butterscotch, calcium citrate, camphor, caramel, cherry, cherry cream, chocolate, cinnamon, bubble gum, citrus, citrus punch, citrus cream, cotton candy, cocoa, cola, cool cherry, cool citrus, cyclamate, cylamate, dextrose, eucalyptus, eugenol, fructose, fruit punch, ginger, glycyrrhetinate, glycyrrhiza (licorice) syrup, grape, grapefruit, honey, isomalt, lemon, lime, lemon cream, monoammonium glyrrhizinate (MagnaSweet®), maltol, mannitol, maple, marshmallow, menthol, mint cream, mixed berry, neohesperidine DC, neotame, orange, pear, peach, peppermint, peppermint cream, Prosweet® Powder, raspberry, root beer, rum, saccharin, safrole, sorbitol, spearmint, spearmint cream, strawberry, strawberry cream, stevia, sucralose, sucrose, sodium saccharin, saccharin, aspartame, acesulfame potassium, mannitol, talin, sucralose, sorbitol, swiss cream, tagatose, tangerine, thaumatin, tutti fruitti, vanilla, walnut, watermelon, wild cherry, wintergreen, xylitol, or any combination of these flavoring ingredients, e.g., anise-menthol, cherry-anise, cinnamon-orange, cherry-cinnamon, chocolate-mint, honey-lemon, lemon-lime, lemon-mint, menthol-eucalyptus, orange-cream, vanilla-mint, and mixtures thereof. In some embodiments, the aqueous liquid dispersion can comprise a sweetening agent or flavoring agent in a concentration ranging from about 0.001% to about 1.0% the volume of the aqueous dispersion. In some embodiments, the aqueous liquid dispersion can comprise a sweetening agent or flavoring agent in a concentration ranging from about 0.005% to about 0.5% the volume of the aqueous dispersion. In yet some embodiments, the aqueous liquid dispersion can comprise a sweetening agent or flavoring agent in a concentration ranging from about 0.01% to about 1.0% the volume of the aqueous dispersion.

In addition to the additives listed above, the liquid formulations can also include inert diluents commonly used in the art, such as water or other solvents, solubilizing agents, and emulsifiers. Exemplary emulsifiers are ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butyleneglycol, dimethylformamide, sodium lauryl sulfate, sodium docusate, cholesterol, cholesterol esters, taurocholic acid, phosphotidylcholine, oils, such as cottonseed oil, groundnut oil, corn germ oil, olive oil, castor oil, and sesame oil, glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols, fatty acid esters of sorbitan, or mixtures of these substances, and the like.

In some embodiments, the pharmaceutical compositions described herein can be self-emulsifying drug delivery systems (SEDDS). Emulsions are dispersions of one immiscible phase in another, usually in the form of droplets. Generally, emulsions are created by vigorous mechanical dispersion. SEDDS, as opposed to emulsions or microemulsions, spontaneously form emulsions when added to an excess of water without any external mechanical dispersion or agitation. An advantage of SEDDS is that only gentle mixing is required to distribute the droplets throughout the solution. Additionally, water or the aqueous phase can be added just prior to administration, which ensures stability of an unstable or hydrophobic active ingredient. Thus, the SEDDS provides an effective delivery system for oral and parenteral delivery of hydrophobic active ingredients. SEDDS may provide improvements in the bioavailability of hydrophobic active ingredients. Methods of producing self-emulsifying dosage forms are known in the art and include, but are not limited to, for example, U.S. Pat. Nos. 5,858,401, 6,667,048, and 6,960,563, each of which is specifically incorporated by reference.

It is to be appreciated that there is overlap between the above-listed additives used in the aqueous dispersions or suspensions described herein, since a given additive is often classified differently by different practitioners in the field, or is commonly used for any of several different functions. Thus, the above-listed additives should be taken as merely exemplary, and not limiting, of the types of additives that can be included in formulations described herein. The amounts of such additives can be readily determined by one skilled in the art, according to the particular properties desired.

Intranasal Formulations

Intranasal formulations are known in the art and are described in, for example, U.S. Pat. Nos. 4,476,116, 5,116,817 and 6,391,452, each of which is specifically incorporated by reference. Formulations that include a compound of any of Formula (I)-(XXIIIh) which are prepared according to these and other techniques well-known in the art are prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, fluorocarbons, and/or other solubilizing or dispersing agents known in the art. See, for example, Ansel, H. C. et al., Pharmaceutical Dosage Forms and Drug Delivery Systems, Sixth Ed. (1995). Preferably these compositions and formulations are prepared with suitable nontoxic pharmaceutically acceptable ingredients. These ingredients are known to those skilled in the preparation of nasal dosage forms and some of these can be found in REMINGTON: THE SCIENCE AND PRACTICE OF PHARMACY, 21st edition, 2005, a standard reference in the field. The choice of suitable carriers is highly dependent upon the exact nature of the nasal dosage form desired, e.g., solutions, suspensions, ointments, or gels. Nasal dosage forms generally contain large amounts of water in addition to the active ingredient. Minor amounts of other ingredients such as pH adjusters, emulsifiers or dispersing agents, preservatives, surfactants, gelling agents, or buffering and other stabilizing and solubilizing agents may also be present. The nasal dosage form should be isotonic with nasal secretions.

For administration by inhalation, the compounds of any of Formula (I)-(XXIIIh), described herein may be in a form as an aerosol, a mist or a powder. Pharmaceutical compositions described herein are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, such as, by way of example only, gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound described herein and a suitable powder base such as lactose or starch.

Buccal Formulations

Buccal formulations that include compounds of any of Formula (I)-(XXIIIh) may be administered using a variety of formulations known in the art. For example, such formulations include, but are not limited to, U.S. Pat. Nos. 4,229,447, 4,596,795, 4,755,386, and 5,739,136, each of which is specifically incorporated by reference. In addition, the buccal dosage forms described herein can further include a bioerodible (hydrolysable) polymeric carrier that also serves to adhere the dosage form to the buccal mucosa. The buccal dosage form is fabricated so as to erode gradually over a predetermined time period, wherein the delivery of the compound of any of Formula (I)-(XXIIIh), is provided essentially throughout. Buccal drug delivery, as will be appreciated by those skilled in the art, avoids the disadvantages encountered with oral drug administration, e.g., slow absorption, degradation of the active agent by fluids present in the gastrointestinal tract and/or first-pass inactivation in the liver. With regard to the bioerodible (hydrolysable) polymeric carrier, it will be appreciated that virtually any such carrier can be used, so long as the desired drug release profile is not compromised, and the carrier is compatible with the compound of any of Formula (I), (Ia)-(Ic), (IIa)-(IId), (IIIa)-(IIIh), (IVa)-(IVd), (Va)-(Vd), (VIa)-(VIh), (VIIa)-(VIId), (VIIIa)-(VIIIh), (IXa)-(IXd), (Xa)-(Xh), (XIa)-(XIj) or (XIIa)-(XIIh), and any other components that may be present in the buccal dosage unit. Generally, the polymeric carrier comprises hydrophilic (water-soluble and water-swellable) polymers that adhere to the wet surface of the buccal mucosa. Examples of polymeric carriers useful herein include acrylic acid polymers and co, e.g., those known as “carbomers” (Carbopol®, which may be obtained from B.F. Goodrich, is one such polymer). Other components may also be incorporated into the buccal dosage forms described herein include, but are not limited to, disintegrants, diluents, binders, lubricants, flavoring, colorants, preservatives, and the like. For buccal or sublingual administration, the compositions may take the form of tablets, lozenges, or gels formulated in a conventional manner.

Transdermal Formulations

Transdermal formulations described herein may be administered using a variety of devices which have been described in the art. For example, such devices include, but are not limited to, U.S. Pat. Nos. 3,598,122, 3,598,123, 3,710,795, 3,731,683, 3,742,951, 3,814,097, 3,921,636, 3,972,995, 3,993,072, 3,993,073, 3,996,934, 4,031,894, 4,060,084, 4,069,307, 4,077,407, 4,201,211, 4,230,105, 4,292,299, 4,292,303, 5,336,168, 5,665,378, 5,837,280, 5,869,090, 6,923,983, 6,929,801 and 6,946,144, each of which is specifically incorporated by reference in its entirety.

The transdermal dosage forms described herein may incorporate certain pharmaceutically acceptable excipients which are conventional in the art. In some embodiments, the transdermal formulations described herein include at least three components: (1) a formulation of a compound of any of Formula (I); (2) a penetration enhancer; and (3) an aqueous adjuvant. In addition, transdermal formulations can include additional components such as, but not limited to, gelling agents, creams and ointment bases, and the like. In some embodiments, the transdermal formulation can further include a woven or non-woven backing material to enhance absorption and prevent the removal of the transdermal formulation from the skin. In some embodiments, the transdermal formulations described herein can maintain a saturated or supersaturated state to promote diffusion into the skin.

Formulations suitable for transdermal administration of compounds described herein may employ transdermal delivery devices and transdermal delivery patches and can be lipophilic emulsions or buffered, aqueous solutions, dissolved and/or dispersed in a polymer or an adhesive. Such patches may be constructed for continuous, pulsatile, or on demand delivery of pharmaceutical agents. Still further, transdermal delivery of the compounds described herein can be accomplished by means of iontophoretic patches and the like. Additionally, transdermal patches can provide controlled delivery of the compounds of any of Formula (I)-(XXIIIh). The rate of absorption can be slowed by using rate-controlling membranes or by trapping the compound within a polymer matrix or gel. Conversely, absorption enhancers can be used to increase absorption. An absorption enhancer or carrier can include absorbable pharmaceutically acceptable solvents to assist passage through the skin. For example, transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin.

Injectable Formulations

Formulations that include a compound of any of Formula (I)-(XXIIIh), suitable for intramuscular, subcutaneous, or intravenous injection may include physiologically acceptable sterile aqueous or non-aqueous solutions, dispersions, suspensions or emulsions, and sterile powders for reconstitution into sterile injectable solutions or dispersions. Examples of suitable aqueous and non-aqueous carriers, diluents, solvents, or vehicles including water, ethanol, polyols (propyleneglycol, polyethylene-glycol, glycerol, cremophor and the like), suitable mixtures thereof, vegetable oils (such as olive oil) and injectable organic esters such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants. Formulations suitable for subcutaneous injection may also contain additives such as preserving, wetting, emulsifying, and dispensing agents. Prevention of the growth of microorganisms can be ensured by various antibacterial and antifungal agents, such as parabens, chlorobutanol, phenol, sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like. Prolonged absorption of the injectable pharmaceutical form can be brought about by the use of agents delaying absorption, such as aluminum monostearate and gelatin.

For intravenous injections, compounds described herein may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. For other parenteral injections, appropriate formulations may include aqueous or nonaqueous solutions, preferably with physiologically compatible buffers or excipients. Such excipients are generally known in the art.

Parenteral injections may involve bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The pharmaceutical composition described herein may be in a form suitable for parenteral injection as a sterile suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Pharmaceutical compositions for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

Formulations

In certain embodiments, delivery systems for pharmaceutical compounds may be employed, such as, for example, liposomes and emulsions. In certain embodiments, compositions provided herein can also include an mucoadhesive polymer, selected from among, for example, carboxymethylcellulose, carbomer (acrylic acid polymer), poly(methylmethacrylate), polyacrylamide, polycarbophil, acrylic acid/butyl acrylate copolymer, sodium alginate and dextran.

In some embodiments, the compounds described herein may be administered topically and can be formulated into a variety of topically administrable compositions, such as solutions, suspensions, lotions, gels, pastes, medicated sticks, balms, creams or ointments. Such pharmaceutical compounds can contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.

The compounds described herein may also be formulated in rectal compositions such as enemas, rectal gels, rectal foams, rectal aerosols, suppositories, jelly suppositories, or retention enemas, containing conventional suppository bases such as cocoa butter or other glycerides, as well as synthetic polymers such as polyvinylpyrrolidone, PEG, and the like. In suppository forms of the compositions, a low-melting wax such as, but not limited to, a mixture of fatty acid glycerides, optionally in combination with cocoa butter is first melted.

Examples of Methods of Dosing and Treatment Regimens

The compounds described herein can be used in the preparation of medicaments for the inhibition of menin or a homolog thereof, or for the treatment of diseases or conditions that would benefit, at least in part, from inhibition of menin or a homolog thereof. In addition, a method for treating any of the diseases or conditions described herein in a subject in need of such treatment, involves administration of pharmaceutical compositions containing at least one compound of any of Formula (I)-(XXIIIh), described herein, or a pharmaceutically acceptable salt, pharmaceutically acceptable N-oxide, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate thereof, in therapeutically effective amounts to said subject.

The compositions containing the compound(s) described herein can be administered for prophylactic and/or therapeutic treatments. In therapeutic applications, the compositions are administered to a patient already suffering from a disease or condition, in an amount sufficient to cure or at least partially arrest the symptoms of the disease or condition. Amounts effective for this use will depend on the severity and course of the disease or condition, previous therapy, the patient's health status, weight, and response to the drugs, and the judgment of the treating physician. It is considered well within the skill of the art for one to determine such therapeutically effective amounts by routine experimentation (including, but not limited to, a dose escalation clinical trial).

In prophylactic applications, compositions containing the compounds described herein are administered to a patient susceptible to or otherwise at risk of a particular disease, disorder or condition. Such an amount is defined to be a “prophylactically effective amount or dose.” In this use, the precise amounts also depend on the patient's state of health, weight, and the like. It is considered well within the skill of the art for one to determine such prophylactically effective amounts by routine experimentation (e.g., a dose escalation clinical trial). When used in a patient, effective amounts for this use will depend on the severity and course of the disease, disorder or condition, previous therapy, the patient's health status and response to the drugs, and the judgment of the treating physician.

In the case wherein the patient's condition does not improve, upon the doctor's discretion the administration of the compounds may be administered chronically, that is, for an extended period of time, including throughout the duration of the patient's life in order to ameliorate or otherwise control or limit the symptoms of the patient's disease or condition.

In the case wherein the patient's status does improve, upon the doctor's discretion the administration of the compounds may be given continuously; alternatively, the dose of drug being administered may be temporarily reduced or temporarily suspended for a certain length of time (i.e., a “drug holiday”). The length of the drug holiday can vary between 2 days and 1 year, including by way of example only, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 15 days, 20 days, 28 days, 35 days, 50 days, 70 days, 100 days, 120 days, 150 days, 180 days, 200 days, 250 days, 280 days, 300 days, 320 days, 350 days, or 365 days. The dose reduction during a drug holiday may be from 10%-100%, including, by way of example only, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.

Once improvement of the patient's conditions has occurred, a maintenance dose is administered if necessary. Subsequently, the dosage or the frequency of administration, or both, can be reduced, as a function of the symptoms, to a level at which the improved disease, disorder or condition is retained. Patients can, however, require intermittent treatment on a long-term basis upon any recurrence of symptoms.

The amount of a given agent that will correspond to such an amount will vary depending upon factors such as the particular compound, disease or condition and its severity, the identity (e.g., weight) of the subject or host in need of treatment, but can nevertheless be routinely determined in a manner known in the art according to the particular circumstances surrounding the case, including, e.g., the specific agent being administered, the route of administration, the condition being treated, and the subject or host being treated. In general, however, doses employed for adult human treatment will typically be in the range of 0.02-5000 mg per day, or from about 1-1500 mg per day. The desired dose may conveniently be presented in a single dose or as divided doses administered simultaneously (or over a short period of time) or at appropriate intervals, for example as two, three, four or more sub-doses per day.

The pharmaceutical composition described herein may be in unit dosage forms suitable for single administration of precise dosages. In unit dosage form, the formulation is divided into unit doses containing appropriate quantities of one or more compound. The unit dosage may be in the form of a package containing discrete quantities of the formulation. Non-limiting examples are packaged tablets or capsules, and powders in vials or ampoules. Aqueous suspension compositions can be packaged in single-dose non-reclosable containers. Alternatively, multiple-dose reclosable containers can be used, in which case it is typical to include a preservative in the composition. By way of example only, formulations for parenteral injection may be presented in unit dosage form, which include, but are not limited to ampoules, or in multi-dose containers, with an added preservative.

The foregoing ranges are merely suggestive, as the number of variables in regard to an individual treatment regime is large, and considerable excursions from these recommended values are not uncommon. Such dosages may be altered depending on a number of variables, not limited to the activity of the compound used, the disease or condition to be treated, the mode of administration, the requirements of the individual subject, the severity of the disease or condition being treated, and the judgment of the practitioner.

Toxicity and therapeutic efficacy of such therapeutic regimens can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, including, but not limited to, the determination of the LD₅₀ (the dose lethal to 50% of the population) and the ED₅₀ (the dose therapeutically effective in 50% of the population). The dose ratio between the toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD₅₀ and ED₅₀. Compounds exhibiting high therapeutic indices are preferred. The data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED₅₀ with minimal toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.

Combination Treatments

The Menin-MLL inhibitor compositions described herein can also be used in combination with other well known therapeutic reagents that are selected for their therapeutic value for the condition to be treated. In general, the compositions described herein and, in embodiments where combinational therapy is employed, other agents do not have to be administered in the same pharmaceutical composition, and may, because of different physical and chemical characteristics, have to be administered by different routes. The determination of the mode of administration and the advisability of administration, where possible, in the same pharmaceutical composition, is well within the knowledge of the skilled clinician. The initial administration can be made according to established protocols known in the art, and then, based upon the observed effects, the dosage, modes of administration and times of administration can be modified by the skilled clinician.

In certain instances, it may be appropriate to administer at least one Menin-MLL inhibitor compound described herein in combination with another therapeutic agent. By way of example only, if one of the side effects experienced by a patient upon receiving one of the Menin-MLL inhibitor compounds described herein is nausea, then it may be appropriate to administer an anti-nausea agent in combination with the initial therapeutic agent. Or, by way of example only, the therapeutic effectiveness of one of the compounds described herein may be enhanced by administration of an adjuvant (i.e., by itself the adjuvant may have minimal therapeutic benefit, but in combination with another therapeutic agent, the overall therapeutic benefit to the patient is enhanced). Or, by way of example only, the benefit experienced by a patient may be increased by administering one of the compounds described herein with another therapeutic agent (which also includes a therapeutic regimen) that also has therapeutic benefit. In any case, regardless of the disease, disorder or condition being treated, the overall benefit experienced by the patient may simply be additive of the two therapeutic agents or the patient may experience a synergistic benefit.

The particular choice of compounds used will depend upon the diagnosis of the attending physicians and their judgment of the condition of the patient and the appropriate treatment protocol. The compounds may be administered concurrently (e.g., simultaneously, essentially simultaneously or within the same treatment protocol) or sequentially, depending upon the nature of the disease, disorder, or condition, the condition of the patient, and the actual choice of compounds used. The determination of the order of administration, and the number of repetitions of administration of each therapeutic agent during a treatment protocol, is well within the knowledge of the skilled physician after evaluation of the disease being treated and the condition of the patient.

It is known to those of skill in the art that therapeutically-effective dosages can vary when the drugs are used in treatment combinations. Methods for experimentally determining therapeutically-effective dosages of drugs and other agents for use in combination treatment regimens are described in the literature. For example, the use of metronomic dosing, i.e., providing more frequent, lower doses in order to minimize toxic side effects, has been described extensively in the literature Combination treatment further includes periodic treatments that start and stop at various times to assist with the clinical management of the patient.

For combination therapies described herein, dosages of the co-administered compounds will of course vary depending on the type of co-drug employed, on the specific drug employed, on the disease or condition being treated and so forth. In addition, when co-administered with one or more biologically active agents, the compound provided herein may be administered either simultaneously with the biologically active agent(s), or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein in combination with the biologically active agent(s).

In any case, the multiple therapeutic agents (one of which is a compound of Formula (I)-(XXIIIh), described herein) may be administered in any order or even simultaneously. If simultaneously, the multiple therapeutic agents may be provided in a single, unified form, or in multiple forms (by way of example only, either as a single pill or as two separate pills). One of the therapeutic agents may be given in multiple doses, or both may be given as multiple doses. If not simultaneous, the timing between the multiple doses may vary from more than zero weeks to less than four weeks. In addition, the combination methods, compositions and formulations are not to be limited to the use of only two agents; the use of multiple therapeutic combinations are also envisioned.

It is understood that the dosage regimen to treat, prevent, or ameliorate the condition(s) for which relief is sought, can be modified in accordance with a variety of factors. These factors include the disorder from which the subject suffers, as well as the age, weight, sex, diet, and medical condition of the subject. Thus, the dosage regimen actually employed can vary widely and therefore can deviate from the dosage regimens set forth herein.

The pharmaceutical agents which make up the combination therapy disclosed herein may be a combined dosage form or in separate dosage forms intended for substantially simultaneous administration. The pharmaceutical agents that make up the combination therapy may also be administered sequentially, with either therapeutic compound being administered by a regimen calling for two-step administration. The two-step administration regimen may call for sequential administration of the active agents or spaced-apart administration of the separate active agents. The time period between the multiple administration steps may range from, a few minutes to several hours, depending upon the properties of each pharmaceutical agent, such as potency, solubility, bioavailability, plasma half-life and kinetic profile of the pharmaceutical agent. Circadian variation of the target molecule concentration may also determine the optimal dose interval.

In addition, the compounds described herein also may be used in combination with procedures that may provide additional or synergistic benefit to the patient. By way of example only, patients are expected to find therapeutic and/or prophylactic benefit in the methods described herein, wherein pharmaceutical composition of a compound disclosed herein and/or combinations with other therapeutics are combined with genetic testing to determine whether that individual is a carrier of a mutant gene that is known to be correlated with certain diseases or conditions.

The compounds described herein and combination therapies can be administered before, during or after the occurrence of a disease or condition, and the timing of administering the composition containing a compound can vary. Thus, for example, the compounds can be used as a prophylactic and can be administered continuously to subjects with a propensity to develop conditions or diseases in order to prevent the occurrence of the disease or condition. The compounds and compositions can be administered to a subject during or as soon as possible after the onset of the symptoms. The administration of the compounds can be initiated within the first 48 hours of the onset of the symptoms, within the first 6 hours of the onset of the symptoms, or within 3 hours of the onset of the symptoms. The initial administration can be via any route practical, such as, for example, an intravenous injection, a bolus injection, infusion over 5 minutes to about 5 hours, a pill, a capsule, transdermal patch, buccal delivery, and the like, or combination thereof. A compound should be administered as soon as is practicable after the onset of a disease or condition is detected or suspected, and for a length of time necessary for the treatment of the disease, such as, for example, from about 1 month to about 3 months. The length of treatment can vary for each subject, and the length can be determined using the known criteria. For example, the compound or a formulation containing the compound can be administered for at least 2 weeks, between about 1 month to about 5 years, or from about 1 month to about 3 years.

Exemplary Therapeutic Agents for Use in Combination with an Menin-MLL Inhibitor Compound

Where the subject is suffering from or at risk of suffering from an autoimmune disease, an inflammatory disease, or an allergy disease, an Menin-MLL inhibitor compound can be used in with one or more of the following therapeutic agents in any combination: immunosuppressants (e.g., tacrolimus, cyclosporin, rapamicin, methotrexate, cyclophosphamide, azathioprine, mercaptopurine, mycophenolate, or FTY720), glucocorticoids (e.g., prednisone, cortisone acetate, prednisolone, methylprednisolone, dexamethasone, betamethasone, triamcinolone, beclometasone, fludrocortisone acetate, deoxycorticosterone acetate, aldosterone), non-steroidal anti-inflammatory drugs (e.g., salicylates, arylalkanoic acids, 2-arylpropionic acids, N-arylanthranilic acids, oxicams, coxibs, or sulphonanilides), Cox-2-specific inhibitors (e.g., valdecoxib, celecoxib, or rofecoxib), leflunomide, gold thioglucose, gold thiomalate, aurofin, sulfasalazine, hydroxychloroquinine, minocycline, TNF-α binding proteins (e.g., infliximab, etanercept, or adalimumab), abatacept, anakinra, interferon-β, interferon-γ, interleukin-2, allergy vaccines, antihistamines, antileukotrienes, beta-agonists, theophylline, or anticholinergics.

Where the subject is suffering from or at risk of suffering from a B-cell proliferative disorder (e.g., plasma cell myeloma), the subjected can be treated with an Menin-MLL inhibitor compound in any combination with one or more other anti-cancer agents. In some embodiments, one or more of the anti-cancer agents are proapoptotic agents. Examples of anti-cancer agents include, but are not limited to, any of the following: gossyphol, genasense, polyphenol E, Chlorofusin, all trans-retinoic acid (ATRA), bryostatin, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), 5-aza-2′-deoxycytidine, all trans retinoic acid, doxorubicin, vincristine, etoposide, gemcitabine, imatinib (Gleevec®), geldanamycin, 17-N-Allylamino-17-Demethoxygeldanamycin (17-AAG), flavopiridol, LY294002, bortezomib, trastuzumab, BAY 11-7082, PKC412, or PD184352, Taxol™, also referred to as “paclitaxel”, which is a well-known anti-cancer drug which acts by enhancing and stabilizing microtubule formation, and analogs of Taxol™, such as Taxotere™. Compounds that have the basic taxane skeleton as a common structure feature, have also been shown to have the ability to arrest cells in the G2-M phases due to stabilized microtubules and may be useful for treating cancer in combination with the compounds described herein.

Other anti-cancer agents that can be employed in combination with an Menin-MLL inhibitor compound include Adriamycin, Dactinomycin, Bleomycin, Vinblastine, Cisplatin, acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan; cactinomycin; calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; daunorubicin hydrochloride; decitabine; dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin; edatrexate; eflomithine hydrochloride; elsamitrucin; enloplatin; enpromate; epipropidine; epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole hydrochloride; fazarabine; fenretinide; floxuridine; fludarabine phosphate; fluorouracil; flurocitabine; fosquidone; fostriecin sodium; gemcitabine; gemcitabine hydrochloride; hydroxyurea; idarubicin hydrochloride; ifosfamide; ilmofosine; interleukin II (including recombinant interleukin II, or rIL2), interferon α-2a; interferon α-2b; interferon α-n1; interferon α-n3; interferon β-1a; interferon γ-1b; iproplatin; irinotecan hydrochloride; lanreotide acetate; letrozole; leuprolide acetate; liarozole hydrochloride; lometrexol sodium; lomustine; losoxantrone hydrochloride; masoprocol; maytansine; mechlorethamine hydrochloride; megestrol acetate; melengestrol acetate; melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin; mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone hydrochloride; mycophenolic acid; nocodazole; nogalamycin; ormaplatin; oxisuran; pegaspargase; peliomycin; pentamustine; peplomycin sulfate; perfosfamide; pipobroman; piposulfan; piroxantrone hydrochloride; plicamycin; plomestane; porfimer sodium; porfiromycin; prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; simtrazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; sulofenur; talisomycin; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine; thiotepa; tiazofurin; tirapazamine; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine sulfate; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate; vinrosidine sulfate; vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride.

Other anti-cancer agents that can be employed in combination with an Menin-MLL inhibitor compound include: 20-epi-1, 25 dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; aclarubicin; acylfulvene; adecypenol; adozelesin; aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox; amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole; andrographolide; angiogenesis inhibitors; antagonist D; antagonist G; antarelix; anti-dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen; antineoplaston; antisense oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators; apurinic acid; ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin; azatyrosine; baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists; benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate; bropirimine; budotitane; buthionine sulfoximine; calcipotriol; calphostin C; camptothecin derivatives; canarypox IL-2; capecitabine; carboxamide-amino-triazole; carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropinB; cetrorelix; chlorlns; chloroquinoxaline sulfonamide; cicaprost; cis-porphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B; combretastatin A4; combretastatin analogue; conagenin; crambescidin 816; crisnatol; cryptophycin 8; cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine; dehydrodidemnin B; deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone; didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; 9-dioxamycin; diphenyl spiromustine; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol; duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflomithine; elemene; emitefur; epirubicin; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists; etanidazole; etoposide phosphate; exemestane; fadrozole; fazarabine; fenretinide; fdgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fluorodaunorunicin hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin; gallium nitrate; galocitabine; ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; hepsulfam; heregulin; hexamethylene bisacetamide; hypericin; ibandronic acid; idarubicin; idoxifene; idramantone; ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-like growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol, 4-; iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor; leukocyte alpha interferon; leuprolide+estrogen+progesterone; leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin; loxoribine; lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maitansine; mannostatin A; marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; M1F inhibitor; mifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol; mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin; monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1-based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N-substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; neridronic acid; neutral endopeptidase; nilutamide; nisamycin; nitric oxide modulators; nitroxide antioxidant; nitrullyn; O6-benzylguanine; octreotide; okicenone; oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer; ormaplatin; osaterone; oxaliplatin; oxaunomycin; palauamine; palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine; pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol; phenazinomycin; phenyl acetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B; plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor; protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylene conjugate; raf antagonists; raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B1; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A; sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen-binding protein; sizofiran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid; spicamycin D; spiromustine; splenopentin; spongistatin 1; squalamine; stem cell inhibitor; stem-cell division inhibitors; stipiamide; stromelysin inhibitors; sulfmosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans; tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide; tetrachlorodecaoxide; tetrazomine; thaliblastine; thiocoraline; thrombopoietin; thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpurin; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine; triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors; tyrphostins; UBC inhibitors; ubenimex; urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; and zinostatin stimalamer.

Yet other anticancer agents that can be employed in combination with an Menin-MLL inhibitor compound include alkylating agents, antimetabolites, natural products, or hormones, e.g., nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, etc.), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, etc.), or triazenes (decarbazine, etc.). Examples of anti metabolites include but are not limited to folic acid analog (e.g., methotrexate), or pyrimidine analogs (e.g., Cytarabine), purine analogs (e.g., mercaptopurine, thioguanine, pentostatin).

Examples of natural products useful in combination with an Menin-MLL inhibitor compound include but are not limited to vinca alkaloids (e.g., vinblastin, vincristine), epipodophyllotoxins (e.g., etoposide), antibiotics (e.g., daunorubicin, doxorubicin, bleomycin), enzymes (e.g., L-asparaginase), or biological response modifiers (e.g., interferon alpha).

Examples of alkylating agents that can be employed in combination an Menin-MLL inhibitor compound include, but are not limited to, nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, meiphalan, etc.), ethylenimine and methylmelamines (e.g., hexamethlymelamine, thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, semustine, streptozocin, etc.), or triazenes (decarbazine, etc.). Examples of antimetabolites include, but are not limited to folic acid analog (e.g., methotrexate), or pyrimidine analogs (e.g., fluorouracil, floxouridine, Cytarabine), purine analogs (e.g., mercaptopurine, thioguanine, pentostatin.

Examples of hormones and antagonists useful in combination with an Menin-MLL inhibitor compound include, but are not limited to, adrenocorticosteroids (e.g., prednisone), progestins (e.g., hydroxyprogesterone caproate, megestrol acetate, medroxyprogesterone acetate), estrogens (e.g., diethlystilbestrol, ethinyl estradiol), antiestrogen (e.g., tamoxifen), androgens (e.g., testosterone propionate, fluoxymesterone), antiandrogen (e.g., flutamide), gonadotropin releasing hormone analog (e.g., leuprolide). Other agents that can be used in the methods and compositions described herein for the treatment or prevention of cancer include platinum coordination complexes (e.g., cisplatin, carboblatin), anthracenedione (e.g., mitoxantrone), substituted urea (e.g., hydroxyurea), methyl hydrazine derivative (e.g., procarbazine), adrenocortical suppressant (e.g., mitotane, aminoglutethimide).

Examples of anti-cancer agents which act by arresting cells in the G2-M phases due to stabilized microtubules and which can be used in combination with an Menin-MLL inhibitor compound include without limitation the following marketed drugs and drugs in development: Erbulozole (also known as R-55104), Dolastatin 10 (also known as DLS-10 and NSC-376128), Mivobulin isethionate (also known as CI-980), Vincristine, NSC-639829, Discodermolide (also known as NVP-XX-A-296), ABT-751 (Abbott, also known as E-7010), Altorhyrtins (such as Altorhyrtin A and Altorhyrtin C), Spongistatins (such as Spongistatin 1, Spongistatin 2, Spongistatin 3, Spongistatin 4, Spongistatin 5, Spongistatin 6, Spongistatin 7, Spongistatin 8, and Spongistatin 9), Cemadotin hydrochloride (also known as LU-103793 and NSC-D-669356), Epothilones (such as Epothilone A, Epothilone B, Epothilone C (also known as desoxyepothilone A or dEpoA), Epothilone D (also referred to as KOS-862, dEpoB, and desoxyepothilone B), Epothilone E, Epothilone F, Epothilone B N-oxide, Epothilone AN-oxide, 16-aza-epothilone B, 21-aminoepothilone B (also known as BMS-310705), 21-hydroxyepothilone D (also known as Desoxyepothilone F and dEpoF), 26-fluoroepothilone), Auristatin PE (also known as NSC-654663), Soblidotin (also known as TZT-1027), LS-4559—P (Pharmacia, also known as LS-4577), LS-4578 (Pharmacia, also known as LS-477—P), LS-4477 (Pharmacia), LS-4559 (Pharmacia), RPR-112378 (Aventis), Vincristine sulfate, DZ-3358 (Daiichi), FR-182877 (Fujisawa, also known as WS-9885B), GS-164 (Takeda), GS-198 (Takeda), KAR-2 (Hungarian Academy of Sciences), BSF-223651 (BASF, also known as ILX-651 andLU-223651), SAH-49960 (Lilly/Novartis), SDZ-268970 (Lilly/Novartis), AM-97 (Armad/Kyowa Hakko), AM-132 (Armad), AM-138 (Armad/Kyowa Hakko), IDN-5005 (Indena), Cryptophycin 52 (also known as LY-355703), AC-7739 (Ajinomoto, also known as AVE-8063A and CS-39.HCl), AC-7700 (Ajinomoto, also known as AVE-8062, AVE-8062A, CS-39-L-Ser.HCl, and RPR-258062A), Vitilevuamide, Tubulysin A, Canadensol, Centaureidin (also known as NSC-106969), T-138067 (Tularik, also known as T-67, TL-138067 and TI-138067), COBRA-1 (Parker Hughes Institute, also known as DDE-261 and WHI-261), H10 (Kansas State University), HI6 (Kansas State University), Oncocidin A1 (also known as BTO-956 and DIME), DDE-313 (Parker Hughes Institute), Fijianolide B, Laulimalide, SPA-2 (Parker Hughes Institute), SPA-1 (Parker Hughes Institute, also known as SPIKET-P), 3-IAABU (Cytoskeleton/Mt. Sinai School of Medicine, also known as MF-569), Narcosine (also known as NSC-5366), Nascapine, D-24851 (Asta Medica), A-105972 (Abbott), Hemiasterlin, 3-BAABU (Cytoskeleton/Mt. Sinai School of Medicine, also known as MF-191), TMPN (Arizona State University), Vanadocene acetylacetonate, T-138026 (Tularik), Monsatrol, lnanocine (also known as NSC-698666), 3-1AABE (Cytoskeleton/Mt. Sinai School of Medicine), A-204197 (Abbott), T-607 (Tuiarik, also known as T-900607), RPR-115781 (Aventis), Eleutherobins (such as Desmethyleleutherobin, Desaetyleleutherobin, lsoeleutherobin A, and Z-Eleutherobin), Caribaeoside, Caribaeolin, Halichondrin B, D-64131 (Asta Medica), D-68144 (Asta Medica), Diazonamide A, A-293620 (Abbott), NPI-2350 (Nereus), Taccalonolide A, TUB-245 (Aventis), A-259754 (Abbott), Diozostatin, (−)—Phenylahistin (also known as NSCL-96F037), D-68838 (Asta Medica), D-68836 (Asta Medica), Myoseverin B, D-43411 (Zentaris, also known as D-81862), A-289099 (Abbott), A-318315 (Abbott), HTI-286 (also known as SPA-110, trifluoroacetate salt) (Wyeth), D-82317 (Zentaris), D-82318 (Zentaris), SC-12983 (NCI), Resverastatin phosphate sodium, BPR-OY-007 (National Health Research Institutes), and SSR-250411 (Sanofi).

Where the subject is suffering from or at risk of suffering from a thromboembolic disorder (e.g., stroke), the subject can be treated with an Menin-MLL inhibitor compound in any combination with one or more other anti-thromboembolic agents. Examples of anti-thromboembolic agents include, but are not limited any of the following: thrombolytic agents (e.g., alteplase anistreplase, streptokinase, urokinase, or tissue plasminogen activator), heparin, tinzaparin, warfarin, dabigatran (e.g., dabigatran etexilate), factor Xa inhibitors (e.g., fondaparinux, draparinux, rivaroxaban, DX-9065a, otamixaban, LY517717, or YM150), ticlopidine, clopidogrel, CS-747 (prasugrel, LY640315), ximelagatran, or BIBR 1048.

Kits/Articles of Manufacture

For use in the therapeutic applications described herein, kits and articles of manufacture are also described herein. Such kits can include a carrier, package, or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the containeds) including one of the separate elements to be used in a method described herein. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers can be formed from a variety of materials such as glass or plastic.

The articles of manufacture provided herein contain packaging materials. Packaging materials for use in packaging pharmaceutical products are well known to those of skill in the art. See, e.g., U.S. Pat. Nos. 5,323,907, 5,052,558 and 5,033,252. Examples of pharmaceutical packaging materials include, but are not limited to, blister packs, bottles, tubes, inhalers, pumps, bags, vials, containers, syringes, bottles, and any packaging material suitable for a selected formulation and intended mode of administration and treatment. A wide array of formulations of the compounds and compositions provided herein are contemplated as are a variety of treatments for any disease, disorder, or condition that would benefit by inhibition of menin, or in which menin is a mediator or contributor to the symptoms or cause.

For example, the containeds) can include one or more compounds described herein, optionally in a composition or in combination with another agent as disclosed herein. The container(s) optionally have a sterile access port (for example the container can be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). Such kits optionally comprising a compound with an identifying description or label or instructions relating to its use in the methods described herein.

A kit will typically may include one or more additional containers, each with one or more of various materials (such as reagents, optionally in concentrated form, and/or devices) desirable from a commercial and user standpoint for use of a compound described herein. Non-limiting examples of such materials include, but not limited to, buffers, diluents, filters, needles, syringes; carrier, package, container, vial and/or tube labels listing contents and/or instructions for use, and package inserts with instructions for use. A set of instructions will also typically be included.

A label can be on or associated with the container. A label can be on a container when letters, numbers or other characters forming the label are attached, molded or etched into the container itself; a label can be associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert. A label can be used to indicate that the contents are to be used for a specific therapeutic application. The label can also indicate directions for use of the contents, such as in the methods described herein.

In certain embodiments, the pharmaceutical compositions can be presented in a pack or dispenser device which can contain one or more unit dosage forms containing a compound provided herein. The pack can for example contain metal or plastic foil, such as a blister pack. The pack or dispenser device can be accompanied by instructions for administration. The pack or dispenser can also be accompanied with a notice associated with the container in form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the drug for human or veterinary administration. Such notice, for example, can be the labeling approved by the U.S. Food and Drug Administration for prescription drugs, or the approved product insert. Compositions containing a compound provided herein formulated in a compatible pharmaceutical carrier can also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

EXAMPLES

The following specific and non-limiting examples are to be construed as merely illustrative, and do not limit the present disclosure in any way whatsoever. Without further elaboration, it is believed that one skilled in the art can, based on the description herein, utilize the present disclosure to its fullest extent. All publications cited herein are hereby incorporated by reference in their entirety. Where reference is made to a URL or other such identifier or address, it is understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.

The examples below as well as throughout the application, the following abbreviations have the following meanings. If not defined, the terms have their generally accepted meanings.

-   -   aq=aqueous     -   Boc=tert-butyloxycarbonyl     -   Z-BuOH=tertiary butanol     -   DCE=1,2-dichloroethane     -   DCM=dichloromethane     -   DIAD=diisopropyl azodicarboxylate     -   DIEA or DIPEA=N,N-diisopropylethylamine     -   DMAP=dimethylaminopyridine     -   DMF=dimethylformamide     -   DMSO=dimethylsulfoxide     -   ESI=electron spray ionization     -   EA=ethyl acetate     -   g=gram     -   HCl=hydrogen chloride     -   HPLC=high performance liquid chromatography     -   hr=hour     -   ¹H NMR=proton nuclear magnetic resonance     -   IPA=isopropyl alcohol     -   KOAc=potassium acetate     -   LC-MS=liquid chromatography mass spectroscopy     -   M=molar     -   MeCN=acetonitrile     -   MeOH=methanol     -   mg=milligram     -   min=minute     -   ml=milliliter     -   mM=millimolar     -   mmol=millimole     -   m.p.=melting point     -   MS=mass spectrometry     -   m/z=mass-to-charge ratio     -   N=normal     -   NIS=N-iodosuccinimide     -   nM=nanomolar     -   nm=nanometer     -   Pd(dppf)Cl₂=[1,1′-Bis(diphenylphosphino)ferrocene]dichloropalladium(II)     -   PE=petroleum ether     -   PyBOP=benzotriazol-1-yl-oxytripyrrolidinophosphonium         hexafluorophosphate     -   quant.=quantitative     -   RP=reverse phase     -   rt or r.t.=room temperature     -   Sat.=saturated     -   TEA=triethylamine     -   TFA=trifluoroacetic acid     -   pE=microliter     -   μM=Micromolar         General Methods

All solvents used were commercially available and were used without further purification. Reactions were typically run using anhydrous solvents under an inert atmosphere of nitrogen.

Liquid Chromatography-Mass Spectrometry Method A

Total ion current (TIC) and DAD UV chromatographic traces together with MS and UV spectra associated with the peaks were taken on a UPLC/MS Acquity™ system equipped with PDA detector and coupled to a Waters single quadrupole mass spectrometer operating in alternated positive and negative electrospray ionization mode. [LC/MS-ES (+/−): analyses performed using an Acquity UPLC™ CSH, C18 column (50×2.1 mm, 1.7 μm particle size), column temperature 40° C., mobile phase: A-water+0.1% HCOOH/B—CH₃CN+0.1% HCOOH, flow rate: 1.0 mL/min, runtime=2.0 min, gradient: t=0 min 3% B, t=1.5 min 99.9% B, t=1.9 min 99.9% B, t=2.0 min 3% B, stop time 2.0 min. Positive ES 100-1000, Negative ES 100-1000, UV detection DAD 210-350 nm.

Liquid Chromatography—Mass Spectrometry Method B

Total ion current (TIC) and DAD UV chromatographic traces together with MS and UV spectra associated with the peaks were taken on a UPLC/MS Acquity™ system equipped with PDA detector and coupled to a Waters single quadrupole mass spectrometer operating in alternated positive and negative electrospray ionization mode. [LC/MS-ES (+/−): analyses performed using an Acquity UPLC™ BEH, C18 column (50×2.1 mm, 1.7 mm particle size), column temperature 40° C., mobile phase: A-0.1% v/v aqueous ammonia solution pH 10/B-CH₃CN, flow rate: 1.0 mL/min, runtime=2.0 min, gradient: t=0 min 3% B, t=1.5 min 99.9% B, t=1.9 min 99.9% B, t=2.0 min 3% B, stop time 2.0 min. Positive ES 100-1000, Negative ES 100-1000, UV detection DAD 210-350 nm.

Analytical Methods

¹H Nuclear magnetic resonance (NMR) spectroscopy was carried out using one of the following instruments: a Bruker Avance 400 instrument equipped with probe DUAL 400 MHz SI, a Bruker Avance 400 instrument equipped with probe 6 SI 400 MHz 5 mm ¹H-¹³C ID, a Bruker Avance III 400 instrument with nanobay equipped with probe Broadband BBFO 5 mm direct, a 400 MHz Agilent Direct Drive instrument with ID AUTO-X PFG probe, all operating at 400 MHz, or an Agilent VNMRS500 Direct Drive instrument equipped with a 5 mm Triple Resonance ¹H{¹³C/¹⁵N} cryoprobe operating at 500 MHz. The spectra were acquired in the stated solvent at around room temperature unless otherwise stated. In all cases, NMR data were consistent with the proposed structures. Characteristic chemical shifts (δ) are given in parts-per-million using conventional abbreviations for designation of major peaks: e.g. s, singlet; d, doublet; t, triplet; q, quartet; dd, doublet of doublets; dt, doublet of triplets; br, broad.

Where thin layer chromatography (TLC) has been used it refers to silica gel TLC using silica gel F254 (Merck) plates, Rf is the distance travelled by the compound divided by the distance travelled by the solvent on a TLC plate. Column chromatography was performed using an automatic flash chromatography (Biotage SP1 or Isolera) system over Biotage silica gel cartridges (KP-Sil or KP-NH) or in the case of reverse phase chromatography over Biotage C18 cartridges (KP-C18).

Generic Synthetic Scheme

wherein Cy, L, R¹, R², R⁴, and n are as described herein.

EXAMPLES Example 1 Preparation of 1-(4-(4-(4-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl)phenyl)-3-(3-(pyridin-3-yl)isoxazol-5-yl)urea

Step 1. Preparation of Intermediate 1

The title compound Intermediate 1 is prepared following the steps depicted in the above reaction scheme.

Step 2. Preparation of Intermediate 2

The title compound Intermediate 2 is prepared following the steps depicted in the above reaction scheme.

Step 3. Preparation of Compound 1

The synthesis of compound 1 is prepared following a similar procedure to compound 2 (Example 2). Crude residue was purified by pre-HPLC (CH₃CN/H₂O with 0.05% NH₄OH as mobile phase) to give compound 1, 1-(4-(4-(4-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl)phenyl)-3-(3-(pyridin-3-yl)isoxazol-5-yl)urea (13 mg, 0.03 mmol) as an off-white solid. ¹H NMR (400 MHz, DMSO-d₆) δ (ppm) 12.67 (s, 1H, NH), 9.19 (s, 1H, NH), 9.03 (s, 1H), 8.80 (s, 1H), 8.67 (s, 1H), 8.34 (m, 2H), 8.23 (d, J=6.2 Hz, 1H), 8.00-7.98 (m, 2H), 7.66 (d, J=7.7 Hz, 2H), 7.53 (m, 1H), 7.44-7.40 (m, 2H), 7.35 (s, 1H), 6.64 (s, 1H), 6.54 (s, 1H). +ES MS (calcd. for C₂₇H₁₉FN₇O₂, M+H) 491.50, found 492.16. Purity by HPLC 96.2% (t_(R)=6.92 min).

Example 2 Preparation of 1-(4-(4-morpholino-7H-pyrrolo[2,3-d]pyrimidin-6-yl)phenyl)-3-(3-(pyridin-3-yl)isoxazol-5-yl)urea

Step 1. Preparation of A-0002-NH2

A mixture of A-SM01 (2.8 g, 10 mmol), 4-aminophenylboronic acid hydrochloride (2.07 g, 12 mmol), PdCl₂dppf.DCM (0.92 g, 1.0 mmol) and sodium carbonate (3.18 g, 30 mmol) in dioxane/water (100 mL, 5:1) was stirred at 80° C. for 16 h under nitrogen. After cooling to rt, morpholine (3.6 g, 40 mmol) was added and the mixture was stirred at reflux for another 16 h. The mixture was concentrated and the residue was purified by reverse phase (CH₃CN/H₂O with 0.05% NH₄OH as mobile phase) to give A-0002-NH2 as a brown solid (1.2 g, Y: 40%). ESI-MS (M+H)⁺: 296.1.

¹H NMR (400 MHz, DMSO-d₆) δ: 11.94 (s, 1H), 8.13 (s, 1H), 7.57 (d, J=7.6 Hz, 2H), 6.84 (s, 1H), 6.59 (d, J=7.6 Hz, 2H), 5.32 (s, 2H), 3.84-3.74 (m, 8H).

Step 2. Preparation of A-SM02

A mixture of 30510-18-0 (1.0 g, 6.8 mmol) and hydroxylamine hydrochloride (0.57 g, 8.2 mmol) in aqueous sodium hydroxide (12 mL. 1M) was stirred at 100° C. for 16 h. After cooling to rt, the solid was collected by filtration and the filter cake was washed with water (15 mL) and dried to give A-SM02 as grey solid (440 mg, Y: 44%). ESI-MS (M+H)⁺: 162.1.

¹H NMR (400 MHz, DMSO-d₆) δ: 8.95 (s, 1H), 8.64 (d, J=3.6 Hz, 1H), 8.12 (d, J=8.0 Hz, 1H), 7.51-7.48 (m, 1H), 6.93 (s, 2H), 5.52 (s, 1H).

Step 3. Preparation of Compound 2

To a solution of A-SM02 (161 mg, 1.0 mmol) and TEA (303 mg, 3.0 mmol) in DCM (10 mL) was added triphosgene (297 mg, 1.0 mmol). The mixture was stirred at rt for 1 h. The precipitate was collected and washed with DCM (10 mmol). The solid was mixed with THF (10 mL) and followed by addition of potassium carbonate (212 mg, 2.0 mmol) and A-0002-NH₂ (295 mg, 1.0 mmol). The resultant mixture was stirred at rt for 2 h. The mixture was concentrated and the residue was triturated with water (10 mL). The solid was dissolved in DMSO and purified by pre-HPLC (CH₃CN/H₂O with 0.05% NH₄OH as mobile phase) to give Compound 2 as a brown solid (51 mg, Y: 10%).

¹H NMR (400 MHz, DMSO-d₆) δ: 12.18 (s, 1H), 10.46 (br, 1H), 9.07 (s, 2H), 8.70 (d, J=4.0 Hz, 1H), 8.25 (d, J=8.0 Hz, 1H), 8.18 (s, 1H), 7.88 (d, J=8.8 Hz, 2H), 7.58-7.53 (m, 3H), 7.11 (s, 1H), 6.71 (s, 1H), 3.89-3.76 (m, 8H). +ES MS (calcd. for C₂₅H₂₃N₈O₃, M+H) 483.19, found 483.32. Purity by HPLC 92.3% (t_(R)=8.59 min).

Example 3 Preparation of 1-(4-(4-cyclopropylmethoxy-7H-pyrrolo[2,3-d]pyrimidin-6-yl)phenyl)-3-(3-(pyridin-3-yl)isoxazol-5-yl)urea

Step 1. Preparation of A-0001

To a solution of cyclopropylmethanol (10.8 g, 150 mmol) in dry DMSO (50 mL) was added NaH (6.0 g, 150 mmol) in three portions. The mixture was stirred at rt for 30 min followed by addition of A-SM01 (7.65 g, 50 mmol). The resultant mixture was stirred at 60° C. for 24 h. After cooling to rt, the mixture was diluted with water (100 mL). The precipitate was filtered and the cake was washed with water (100 mL) and dried to under vacuum to give title product as a light brown solid (6.5 g, Y: 67%). ESI-MS (M+H)⁺: 190.1.

Step 2. Preparation of A-0002

To a solution of A-0001 (8.39 g, 44 mmol) in dry DMF (80 mL) was added NaH (1.94 g, 48.5 mmol) at 0° C. in three portions. The mixture was stirred at this temperature for 30 min followed by addition of benzenesulfonyl chloride (7.57 g, 48.5 mmol). The resultant mixture was stirred at rt for 3 h. The mixture was quenched with aqueous sat. ammonium chloride (100 mL). The precipitate was filtered and the cake was washed with water (50 mL) and dried to under vacuum to give title product as a light brown solid (10 g, Y: 82%). ESI-MS (M+H)⁺: 330.1.

¹H NMR (400 MHz, DMSO-d₆) δ: 8.54 (s, 1H), 7.83 (d, J=7.6 Hz, 2H), 7.83 (d, J=3.6 Hz, 1H), 7.78-7.75 (m, 1H), 7.68-7.64 (m, 2H), 6.84 (d, J=4.0 Hz, 1H), 4.31 (d, J=7.2 Hz, 2H), 1.31-1.28 (m, 1H) 0.58-0.53 (m, 2H), 0.38-0.34 (m, 2H).

Step 3. Preparation of A-0003

To a solution of A-0002 (6.58 g, 20 mmol) in dry THF (100 mL) was added a solution of LDA (24 mmol, 12 mmol, 2M) at −78° C. under nitrogen. The mixture was stirred at this temperature for 30 min followed by addition of solid iodine (6.10 g, 24 mmol). The resultant mixture was stirred at −78° C. for 5 min and then rt for 16 h. The mixture was quenched with aqueous sat. ammonium chloride (100 mL) and extracted with EA (100 mL, ×2). The combined organic phases were washed with sat. Na₂S₂O₃ (100 mL×2), brine (100 mL) and dried over sodium sulfate. The solvent was removed to give title product as a brown solid (10 g, yield: 82%), which was used to next step without further purification. ESI-MS (M+H)⁺: 456.1.

Step A. Preparation of A-004

A mixture of A-0003 (4.56 g, 10 mmol), 4-aminophenylboronic acid hydrochloride (2.07 g, 12 mmol), PdCl₂dppf.DCM (0.92 g, 1.0 mmol) and sodium carbonate (2.12 g, 20 mmol) in dioxane/water (100 mL, 5:1) was stirred at 100° C. for 16 h under nitrogen. After cooling to rt, the residue was triturated with THF/Water (100 mL, 1:1) and the solid was collected and dried to give crude title product (4.1 g), which was used to next step without further purification. ESI-MS (M+H)⁺: 420.1.

Step 5. Preparation of A-0005

To a suspension of A-0004 (504 mg, 1.2 mmol) in THF/MeOH/water (30 mL, 1:1:1) was slowly added NaOH (192 mg, 4.8 mmol). The mixture was stirred at rt for 16 h. The mixture was concentrated and the residue was purified by reverse phase column (CH₃CN/H₂O with 0.05% NH₄OH as mobile phase) to give title product as a brown solid (200 mg, Y: 59%). ESI-MS (M+H)⁺: 281.1.

¹H NMR (400 MHz, DMSO-d₆) δ: 12.20 (s, 1H), 8.25 (s, 1H), 7.59 (d, J=8.4 Hz, 2H), 6.63-6.60 (m, 3H), 5.36 (s, 2H), 4.30 (d, J=7.2 Hz, 2H), 1.35-1.31 (m, 1H) 0.61-0.57 (m, 2H), 0.40-0.36 (m, 2H).

Step 6. Preparation of Compound 3

The synthesis of compound 3 used a similar procedure to compound 2 (Example 2). Crude residue was purified by pre-HPLC (CH₃CN/H₂O with 0.05% NH₄OH as mobile phase) to give compound 3 as a brown solid (21 mg, Y: 6%). ESI-MS (M+H)⁺: 468.1.

¹H NMR (400 MHz, DMSO-d₆) δ: 12.42 (s, 1H), 10.49 (s, 1H), 9.09-9.05 (m, 2H), 8.69 (d, J=4.0 Hz, 1H), 8.33 (s, 1H), 8.24 (d, J=8.0 Hz, 1H), 7.90 (d, J=8.8 Hz, 2H), 7.60-7.54 (m, 3H), 6.92 (s, 1H), 6.69 (s, 1H), 4.33 (d, J=7.2 Hz, 2H), 1.36-1.32 (m, 1H), 0.62-0.57 (m, 2H), 0.42-0.38 (m, 2H).

Example 4 Preparation of 1-(4-(4-cyclopropyl-7H-pyrrolo[2,3-d]pyrimidin-6-yl)phenyl)-3-(3-(pyridin-3-yl)isoxazol-5-yl)urea

The title compound, Compound 4, can be prepared following the steps depicted in the above reaction scheme.

Example 5 Preparation of N-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-2-[3-(pyridin-3-yl)-1,2-oxazol-5-yl]acetamide

Step 1. Preparation of Intermediate 1

4-chloro-6-iodo-7H-pyrrolo[2,3-d]pyrimidine (5 g, 17.9 mmol) was dissolved in 1-butanol (90 ml) and morpholine (4.7 ml, 53.8 mmol) was added. The mixture was stirred at reflux for 3 h then it was cooled to rt and filtered. The solid obtained was washed with 20 ml of cyclohexane to afford 4-{6-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl}morpholine (5.85 g, Y=99%)

¹H NMR (400 MHz, DMSO-d6) δ ppm 3.71 (m, 4H) 3.79 (m, 4H) 6.88 (s, 1H) 8.09 (s, 1H) 12.30 (br. s., 1H).

LC-MS (Method A): purity: 97% m/z=331.05 [M+H]⁺, 0.49 min.

4-{6-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl}morpholine (Intermediate 1, 2 g, 6.06 mmol), (4-aminophenyl) boronic acid hydrochloride (1.47 g, 8.48 mol) and K₃PO₄ (3.85 g, 18.18 mmol) were dissolved in DMA/Water (50 ml/40 ml). [1,1′-Bis(diphenylphosphino)ferrocene]dichloropalladium(II) (440 mg, 0.6 mmol) was added and the mixture was heated at 100° C. for 1h. UPLC analysis showed complete conversion. Water (200 ml) was added and the solid obtained was filtered and washed with 30 ml of diethyl ether to afford 4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (1.7 g, Y=95%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.72-3.77 (m, 4H) 3.83-3.87 (m, 4H) 5.30 (s, 2H) 6.54-6.66 (s, 2H) 6.83 (s, 1H) 7.58 (d, J=8.53 Hz, 2H) 8.09-8.19 (m, 1H) 11.90 (br. s., 1H). Purity 90% by NMR.

Step 2. Preparation of Intermediate 2

To a solution of nicotinaldehyde (2 g, 18.66 mmol) in ethanol/water (1/1=20 mL/20 mL) was added sodium acetate (4.6 g, 56 mmol) and hydroxylamine hydrochloride (1.42 g, 20.54 mmol). The resulting mixture was stirred at RT for 3 hours. UPLC analysis revealed that reaction was finished and the solution was concentrated up to 20 mL. A white precipitate was observed. It was filtered and washed with water (2×10 mL), dried under vacuum to give N-(pyridin-3-ylmethylidene)hydroxylamine (1.72 g, 75% yield).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 7.40-7.47 (m, 1H) 7.99 (dt, J=7.92, 1.8 Hz, 1H) 8.21 (s, 1H) 8.54-8.60 (m, 1H) 8.76 (d, J=1.8 Hz, 1H) 11.53 (s, 1H).

LC-MS (Method A): Purity: 96%, m/z=122.8 [M+H]⁺, 0.20 min.

N-(pyridin-3-ylmethylidene)hydroxylamine (Intermediate 5, 1.72 g, 14.08 mmol) was dissolved in dry DMF (13 mL) and cooled at 0° C. Then/V-chlorosuccinimide (2.25 g, 16.9 mmol) was added and the resulting mixture was stirred at RT for 16 hrs. UPLC analysis revealed that reaction was finished and the mixture was diluted with ethyl acetate (240 mL). The mixture was washed with brine (3×40 mL). The organic layers were collected, dried over Na₂SO₄, filtered and concentrated under vacuum to give N-hydroxypyridine-3-carbonimidoyl chloride (2 g, 91% yield) as orange solid. ¹H NMR (400 MHz, DMSO-d₆) δ ppm 7.51-7.58 (m, 1H) 8.17 (dt, J=8.14, 1.98 Hz, 1H) 8.69 (dd, J=4.84, 1.6 Hz, 1H) 8.97 (d, J=1.6 Hz, 1H) 12.71 (s, 1H).

LC-MS (Method A): Purity: 94%, m/z=156.9 [M+H]⁺, 0.44 min.

To a solution of N-hydroxypyridine-3-carbonimidoyl chloride (Intermediate 6, 1.35 g, 8.62 mmol) in DCM was added triethyl amine (1.8 ml, 12.9 mmol) and 3-butyn-1-ol (0.98 ml, 12.9 mmol). The resulting red solution was stirred at RT for 5 hrs. Then the solution was concentrated under vacuum to give crude compound that was purified by chromatography (Biotage, 50 g NH, DCM/MeOH=98/2) to give 2-[3-(pyridin-3-yl)-1,2-oxazol-5-yl]ethan-1-ol (553 mg, 34%) as a yellow oil.

¹H NMR (400 MHz, DMSO-d) δ ppm 2.93-3.03 (m, 2H), 3.72-3.83 (m, 2H), 6.95 (s, 1H) 7.55 (ddd, J=7.97, 4.83, 0.75 Hz, 1H) 8.24 (dt, J=7.97, 1.91 Hz, 1H) 8.69 (dd, J=4.77, 1.76 Hz, 1H) 9.05 (dd, J=2.3, 0.75 Hz, 1H).

LC-MS (Method A): Purity: 92%, m/z=190.95 [M+H]⁺, 0.36 min.

To a solution of 2-[3-(pyridin-3-yl)-1,2-oxazol-5-yl]ethan-1-ol (Int. 7, 500 mg, 2.6 mmol) in acetone at 0° C. Jones reagent (2.2 ml) was added and the mixture was stirred at rt overnight. UPLC analysis showed that reaction was complete. The mixture was evaporated in vacuo and dissolved in MeOH (20 ml). SOCl₂ (1 ml) was added dropwise and after 1 h complete formation of methyl ester was observed. The mixture was evaporated in vacuo, DCM (20 ml) was added followed by NaHCO3 sat. Sol. (10 ml) and the biphasic mixture was stirred for 1 h. Organic phase was separated and evaporated in vacuo to afford 270 mg of [3-(pyridin-3-yl)-1,2-oxazol-5-yl]acetic acid methyl ester. This material was dissolved in THF/Water (10 ml:1 ml) and Lithium hydroxide monohydrate (51.96 mg, 1.23 mmol) was added and the mixture was stirred at 60° C. overnight. UPLC analysis showed that reaction was complete so the solvent was evaporated in vacuo and the residue solid was tritured with diethyl ether (10 ml) to afford [3-(pyridin-3-yl)-1,2-oxazol-5-yl]acetic acid Lithium salt (200 mg, 38%).

LC-MS (Method A): Purity: 90%, m/z=205.36 [M+H]⁺, 0.38 min.

Step 3. Preparation of Compound 5

To a solution of 4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (Intermediate 1, 289 mg, 0.98 mmol) and 2-[3-(pyridin-3-yl)-1,2-oxazol-5-yl]acetic acid Lithium salt (Intermediate 2, 200 mg, 0.98 mmol) in dry DMF (10 mL) at 0° C. was added DIPEA (0.682 mL, 3.92 mmol) and HATU (447 mg, 1.17 mmol). The resulting mixture was stirred at rt for 1 h. UPLC analysis showed that reaction was complete, water (30 ml) was added and the mixture was extracted with DCM/MeOH 9:1 (2×50 ml). The organic phases were collected together and washed with NaHCO₃ sat. sol. 30 ml. The organic phase was separated, dried and evaporated in vacuo to afford 250 mg of product that contained 4% w/w of DMF. This solid was triturated with 5 ml of MeOH and then with 6 ml of diethyl ether to afford N-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-2-[3-(pyridin-3-yl)-1,2-oxazol-5-yl]acetamide as a brown solid (167 mg, Y=35%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.70-3.79 (m, 4H) 3.84-3.94 (m, 4H) 4.09 (s, 2H) 7.11 (d, J=8.03 Hz, 2H) 7.57 (dd, J=7.91, 4.89 Hz, 1H) 7.68 (d, J=8.78 Hz, 2H) 7.89 (d, J=8.78 Hz, 2H) 8.18 (s, 1H) 8.28 (dt, J=7.91, 2.07 Hz, 1H) 8.71 (dd, J=4.77, 1.51 Hz, 1H) 9.09 (d, J=1.76 Hz, 1H) 10.54 (s. br., 1H) 12.11-12.32 (s. br., 1H).

Example 6 Preparation of 1-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-3-[4-(propan-2-yl)-3-(pyridin-3-yl)-1,2-oxazol-5-yl]urea

Step 1. Preparation of Intermediate 3

Ethyl pyridine-3-carboxylate (4 g, 26 mmol, 1.8 eq) and 3-methylbutanenitrile (1.25 g, 15 mmol) were mixed together, tBuOK in THF (45 ml, 1 M solution) was slowly added under stirring at room temperature. The resulting mixture was stirred at room temperature overnight, (mix turned dark yellow). iPr₂O (90 ml) was added and the mix was stirred at room temperature for 1 h. The slurry was filtered and the solid obtained was washed with iPr2O (5 ml×2 times). Yellow solid (3.1 g, Y=91%, purity by LC-MS: 95%), Diastereoisomeric mixture E/Z. Used in the next step as it is.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 1.0 (d, J=6.8 Hz, 6H) 1.0 (m, 6H) 3.4 (q, J=7.0 Hz, 1H) 3.6 (spt, J=6.1 Hz, 1H) 7.2 (m, 3H) 7.5 (dt, J=1.7, 1.9 Hz, 1H) 7.8 (dt, J=7.8, 2.0 Hz, 1H) 8.1 (dt, J=1.7, 1.9 Hz, 1H) 8.4 (m, 1H) 8.4 (dd, J=4.8, 1.8 Hz, 1H) 8.7 (dd, J=2.1, 0.9 Hz, 1H) 8.9 (d, J=1.3 Hz, 1H). Mixture E/Z.

LC-MS (Method A): Purity: 95%, m/z=189.16 [M+H]⁺, 0.71 min.

Potassium-2-cyano-3-methyl-1-(pyridin-3-yl)but-1-en-1-olate (Intermediate 9, 3.1 g, 13.7 mmol) was dissolved in NaOH 1 M aq. (60 ml) then Hydroxylamine hydrochloride was added. The resulting mixture was stirred at 100° C. overnight, (mix turned pale yellow). The mixture was cooled to 20° C., stirred for 2h and filtered, the solid obtained was washed with H2O (2×5 ml) and stripped with toluene (2×10 ml). White solid (1.2 g, Y=44%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 1.1 (d, J=7.0 Hz, 6H) 2.6 (spt, J=1.1 Hz, 1H) 6.5 (s, 2H) 7.5 (m, 1H) 7.9 (dt, J=7.9, 1.9 Hz, 1H) 8.6 (d, J=1.5 Hz, 1H) 8.7 (m, 1H).

LC-MS (Method A): Purity: 92%, m/z=204.2 [M+H]⁺, 0.51 min.

4-(propan-2-yl)-3-(pyridin-3-yl)-1,2-oxazol-5-amine (Intermediate 10, 320 mg, 1.57 mmol) was dissolved in THF (3 mL), Pyridine (753 mg, 9.42 mmol) was added and the solution was stirred at room temperature for 10 min, then 2,2,2-trichloroethyl chloroformate (993 mg, 4.71 mmol) was added and the mix was stirred at room temperature for 1 h. UPLC-MS: bis acilated product detected. Na₂CO₃ aq sat solution (4 ml) was added, the mix was stirred for 3h at room temperature. UPLC-MS: desired product 80%. The mix was diluted with DCM and washed with Water. Organic phases were collected and concentrated to afford 2,2,2-trichloroethyl N-[4-(propan-2-yl)-3-(pyridin-3-yl)-1,2-oxazol-5-yl]carbamate, 650 mg, Y=quant.

LC-MS (Method A): Purity: 80%, m/z=377.96 [M+H]⁺, 1.02 min.

Step 2. Preparation of Compound 6

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (Intermediate 1, 220 mg, 0.74 mmol) was dissolved in DMSO (5 ml), TEA (0.202 ml, 1.48 mmol) was added and the mixture was stirred for 10 min. To this solution 2,2,2-trichloroethyl N-[4-(propan-2-yl)-3-(pyridin-3-yl)-1,2-oxazol-5-yl]carbamate (Intermediate 11, 280 mg, 0.74 mmol) was added at room temperature. Resulting suspension was stirred at 100° C. for 5 h. the mixture was cooled to rt then Water (10 ml) was added, precipitate was collected and washed with water (4 ml) and Et₂O (5 ml), the solid was extracted with MeOH (30 ml×6). Methanolic solution was collected and concentrated affording the title compound. (106 mg, Y=28%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 1.2 (d, J=7.0 Hz, 6H) 2.8 (t, 7.1 Hz, 1H) 3.8 (m, 4H) 3.9 (m, 4H) 7.1 (d, J=1.5 Hz, 1H) 7.6 (m, 3H) 7.9 (d, J=8.8 Hz, 2H) 8.0 (dt, J=7.9, 1.9 Hz, 1H) 8.2 (m, 1H) 8.7 (m, 2H) 9.3 (br. s., 1H) 9.5 (br. s., 1H) 12.1 (s, 1H).

Example 7 Preparation of 1-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-(propan-2-yl)phenyl}-3-[3-(pyridin-3-yl)-1,2-oxazol-5-yl]urea

Step 1. Preparation of Intermediate 4

4-bromo-2-(propan-2-yl)aniline (0.5 g, 2.3 mmol), Bis(pinacolato)diboron (880 mg, 3.45 mmol) and Potassium Acetate (0.564 g, 5.75 mmol) were dissolved in Dioxane (20 ml), then [1,1′-bis(diphenylphosphino) ferrocene] dichloropalladium (II) (0.085 g, 0.115 mmol) was added. The mixture was heated to 105° C. under inert atmosphere for 4h. UPLC-MS: Reaction completed. The mix was concentrated, water (20 ml) was added and extracted with DCM (30 ml×2), the organic layer was collected and concentrated. Crude was chromatographed KP-Sil 25 g (Cy/AcOEt 100:00 to 60:40). yellow solid (560 mg, 93%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 1.1 (d, J=6.8 Hz, 6H) 1.3 (s, 12H) 2.9 (m, 1H) 5.3 (s, 2H) 6.6 (m, 1H) 7.2 (dd, J=7.9, 1.4 Hz, 1H) 7.3 (d, J=1.0 Hz, 1H). LC-MS (Method A): Purity: 98%, m/z=262.3 [M+H]⁺, 1.13 min.

A mixture of 4-chloro-6-iodo-7H-pyrrolo[2,3-d]pyrimidine (0.5 g, 1.79 mmol), 2-(propan-2-yl)-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline (Intermediate 11, 0.56 g, 2.14 mmol), PdCl₂dppf (0.131 g, 0.179 mmol) and sodium carbonate (0.57 g, 5.37 mmol) in dioxane/water (18 mL, 5:1) was stirred at 90° C. for 16 h under nitrogen. Morpholine (623 mg, 7.16 mmol) was added and the mixture was stirred at 100° C. for 12 h. Water (40 ml) was added and the mixture was extracted with CH₂Cl₂ (100 ml×2), the organic phases were collected and concentrated. Crude was purified over a KP-Sil 25 g DCM-EtOH 100:00 to 70:30, Brown solid (360 mg, 58%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 1.2 (d, J=6.8 Hz, 6H) 3.0 (m, 1H) 3.7 (m, 4H) 3.8 (m, 4H) 5.1 (m, 2H) 6.7 (m, 1H) 6.8 (m, 1H) 7.4 (m, 1H) 7.6 (m, 1H) 8.1 (s, 1H) 12.0 (s, 1H).

LC-MS (Method A): Purity: 97%, m/z=338.3 [M+H]⁺, 0.57 min.

Step 2. Preparation of Compound 7

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-(propan-2-yl)aniline (Intermediate 4, 310 mg, 0.919 mmol) was added to a solution of CDI (253 mg, 1.56 mmol) in DCM (5 ml). Resulting suspension was stirred at RT for 6 h. Check with methanol, 100% conversion. DMF (5 ml) and 3-(pyridin-3-yl)-1,2-oxazol-5-amine (296 mg, 1.84 mmol) were added then DCM was evaporated by rotary evaporation, the resulting solution was heated at 100° C. for 30 min, reaction completed. Water (10 ml) was added, precipitate was collected and washed with water (4 ml) and DCM (5 ml), the solid was extracted with MeOH (30 ml×6). Methanolic solution was collected and concentrated affording the title compound. 105 mg, Y=22%.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 1.3 (d, J=6.8 Hz, 6H) 3.2 (m, 1H) 3.8 (m, 4H) 3.9 (m, 4H) 6.6 (m, 1H) 7.1 (m, 1H) 7.5 (m, 1H) 7.8 (m, 3H) 8.2 (s, 1H) 8.2 (m, 1H) 8.7 (m, 1H) 9.0 (m, 1H) 10.8 (m, 1H) 12.2 (s, 1H).

Example 8 Preparation of 1-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-3-[3-(pyridin-4-yl)-1,2-oxazol-5-yl]urea

Step 1. Preparation of Intermediate 5

A solution of 3-oxo-3-pyridin-4-ylpropanenitrile (5 g, 34.2 mmol) and hydroxylamine hydrochloride (2.4 g, 34.2 mmol) in NaOH aq. IN (70 mL, 68.4 mmol) was stirred at 100° C. for 24 hrs. UPLC analysis revealed that reaction was finished and the mixture was cooled at 0° C. A yellow precipitate was observed. It was filtered, washed with water (2×5 mL), dried under vacuum to give 3-(pyridin-4-yl)-1,2-oxazol-5-amine (1.59 g, 29% yield) as pale yellow solid.

¹H NMR (400 MHz, DMSO-d) δ ppm 5.5 (s, 1H) 6.9 (s, 2H) 7.7 (m, 2H) 8.7 (m, 2H), Purity by NMR 98%

3-(pyridin-4-yl)-1,2-oxazol-5-amine was dissolved in THF (5 mL), TEA (1.6 ml, 11.9 mmol) was added and the solution was stirred at room temperature for 10 min, then triphosgene (1,76 g, 5.94 mmol) was added and the mix was stirred at room temperature for 20 min. UPLC-MS: quench with MeOH, reaction completed. DCM (15 ml) was added. The yellow precipitate was collected, washed with Et₂O (10 ml, ×3) and dried by rotary evaporation. Yellow solid, 440 mg, Y=98%.

LC-MS (Method A): Quench with MeOH, Purity: 87%, m/z=220.2 [M+H]⁺, 0.40 min.

Step 2. Preparation of Compound 8

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (Intermediate 2, 180 mg, 0.61 mmol) was dissolved in DMSO (5 ml), then TEA (0.16 ml, 1.22 mmol) was added. 4-(5-isocyanato-1,2-oxazol-3-yl)pyridine (114 mg, 0.61 mmol) was added and the resulting solution was stirred at RT for 6 h. UPLC Check, quench with methanol: 100% conversion.

Water (10 ml) was added, precipitate was collected and washed with water (4 ml) and Et2O (25 ml). The solid was collected affording the title compound, 107 mg, Y=36%.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.8 (d, J=4.8 Hz, 4H) 3.9 (m, 4H), 6.5 (br. s., 1H) 7.1 (s, 1H) 7.6 (d, J=8.5 Hz, 2H) 7.8 (m, 3H) 8.2 (s, 1H) 8.7 (m, 2H) 8.9 (br. s., 1H) 10.5 (m, 1H) 12.1 (br. s., 1H)

LC-MS (Method A): Purity: 96%, m/z=483.56 [M+H]⁺, 0.53 min.

Example 9 Preparation of 1-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-3-[3-(pyridin-3-yl)-1H-pyrazol-5-yl]urea

Step 1. Preparation of Intermediate 6

A solution of 3-oxo-3-(pyridin-3-yl)propanenitrile (2 g, 13.6 mmol) and Hydrazine monohydrate (748 mg, 15 mmol) in NaOH aq. IN (30 mL, 30 mmol) was stirred at 100° C. for 20 hrs. UPLC analysis revealed that reaction was finished, NH₄Cl (1.8 g) was added and the mixture was cooled at 0° C. A yellow precipitate was observed. It was filtered, washed with water (2×5 mL), dried under vacuum to give 3-(pyridin-3-yl)-1H-pyrazol-5-amine (1.04 g, 48% yield) as pale yellow solid.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 4.97 (s. br, 2H) 5.82 (s., 1H) 7.40 (m, 1H) 8.01 (dt, J=7.8, 2.0 Hz, 1H) 8.47 (m, 1H) 8.88 (dd, J=2.0, 0.8 Hz, 1H) Purity: 95% by NMR.

Step 2. Preparation of Compound 9

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (Intermediate 2, 350 mg, 0.899 mmol) was added to a solution of CDI (253 mg, 1.56 mmol) in DCM (5 ml). Resulting suspension was stirred at RT for 10 h. Check with methanol 100% conversion. DMF (5 ml) and 3-(pyridin-3-yl)-1H-pyrazol-5-amine (Intermediate 6, 172 mg, 1.08 mmol) were added then DCM was evaporated by rotary evaporation, The resulting solution was heated at 100° C. for 30 min, reaction completed.

Water (15 ml) was added, precipitate was collected and washed with water (4 ml) and Et₂O (5 ml). The solid was washed with CH₂Cl₂ (5 ml) and dried affording the title compound. 284 mg, Y=66% registered as APV214241A.

LC-MS (Method A): m/z=482.15 [M+H]⁺, 0.66 min. Purity: 96%.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.77 (m, 4H) 3.90 (m, 4H) 5.95 (s, 1H) 6.69 (s, 2H) 7.18 (d, J=2.0 Hz, 1H) 7.50 (ddd, J=7.8, 4.8, 0.9 Hz, 1H) 7.82 (d, J=8.8 Hz, 2H) 7.95 (d, J=8.8 Hz, 2H) 8.20 (m, 1H) 8.33 (dt, J=8.1, 1.9 Hz, 1H) 8.60 (dd, J=4.8, 1.8 Hz, 1H) 9.20 (dd, J=2.3, 0.8 Hz, 1H) 10.10 (s, 1H) 12.21 (d, J=1.5 Hz, 1H).

Example 10 Preparation of N-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-2-[3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetamide

Step 1. Preparation of Intermediate 7

Nicotinic acid (6 g, 48.73 mmol), N,O-Dimethylhydroxylamine hydrochloride (4.991 g, 51.17 mmol), HOBt (1.975 g, 14.62 mmol) and A-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (11.21 g, 58.48 mmol) were suspended in ACN (60 mL). NEt₃ (5.128 g, 50.68 mmol, 7 mL) was dropwise added to reaction mixture under N₂ atmosphere. The reaction was stirred at rt overnight.

Water was added and ACN was evaporated under reduced pressure. The aqueous phase was extracted three times with EtOAc. The combined organic phases were washed with H₂O once and, then, with NH₄Cl sat aq (three times), dried over Na₂SO₄ and concentrated under reduced pressure. The crude of reaction was used in the following step without any further purification. (5.1 g, Y=64%).

¹H NMR (400 MHz, DMSO-d6) δ ppm 8.78 (dd, J=2.20, 0.66 Hz, 1H), 8.66-8.70 (m, 1H), 8.00 (dt, J=7.92, 1.98 Hz, 1H), 7.50 (ddd, J=7.92, 4.84, 0.88 Hz, 1H), 3.56 (s, 3H), 3.30 (s, 3H).

LC-MS (Method A): purity: 98% m/z=167.05 [M+H]⁺, 0.34 min.

Sodium hydride (1.20 g, 30.10 mmol, 60% dispersion in mineral oil) was suspended in THF at 0° C. Ethylacetoacetate (3.914 g, 30.10 mmol) was dropwise added at 0° C. (effervescence). The mixture was stirred at 0° C. for 10 minutes (until no effervescence was visible in the flask of reaction) and, then, was cooled to −78° C. n-BuLi (34.61 mmol, 13.84 mL) was dropwise added at −78° C., so that the internal temperature was never higher than −60° C. (time of addition: 10 minutes) and the reaction was stirred at −78° C. for 30 minutes (the mixture turns from light grey to yellowish). Then, N-methoxy-N-methylpyridine-3-carboxamide (5 g, 30.10 mmol) was dropwise added over 10 minutes. The mixture was allowed to warm up to rt and stirred at that temperature overnight. UPLC-MS: reaction completed. Mix was concentrated, HCl aq 0.1 N was added until pH 6 was reached and the mix was extracted with AcOEt (60 ml×2), the organic phases were collected and concentrated. Yellow oil, ethyl 3,5-dioxo-5-(pyridin-3-yl)pentanoate (4.25 g, Y=61%).

Idrazine (257 mg, 252 μL, 8.1 mmol) and ethyl 3,5-dioxo-5-(pyridin-3-yl)pentanoate (2,126 g, 9.0 mmol) were heated at 70° C. for 8 hours in EtOH (10 mL). Then, the mixture was concentrated under reduced pressure. The crude was purified by RP C-18 column chromatography (H₂O/ACN, both with 1% HCOOH=100:00 to 70:30) to give ethyl 2-[3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetate as formate salt (201 mg Y=10%).

¹H NMR (400 MHz, DMSO-d6) δ ppm 1.22 (3H, t, J=7.0 Hz) 3.75 (2H, br. s) 4.12 (2H, m) 6.70 (1H, s) 7.44 (1H, m) 8.12 (1H, d, J=8.1 Hz) 8.15 (1H, s) 8.50 (1H, dd, J=6.4, 1.0 Hz) 8.98 (1H, d, J=1.8 Hz) 12.85 (1H, br. s).

LC-MS (Method A): purity: 91% m/z=232.1 [M+H]⁺, 0.41 min.

LC-MS (Method A): purity: 91% m/z=232.1 [M+H]⁺, 0.41 min.

A solution of ethyl 2-[3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetate (200 mg, 0.86 mmol) in THF (1.5 mL), water (1.5 mL) and methanol (0.5 mL) was treated with LiOH*H₂O (72 mg, 1.72 mmol) and stirred for 3 hours at room temperature. The solution was adjusted to pH 2 with 3 mL HCl aq. 1M, the mixture was concentrated and stripped 3 times with Toluene (5 ml×3). the desired product of sufficient purity for subsequent use without further purification. 3-[5-(carboxymethyl)-1H-pyrazol-3-yl]pyridin-1-ium hydrochloride. (209 mg, quantitative yield). ¹H NMR (400 MHz, DMSO-d6) δ ppm 3.74 (2H, s) 6.90 (1H, s) 7.98 (1H, m) 8.77 (2H, m) 9.23 (1H, s).

LC-MS (Method A): purity: 91% m/z=204.1 [M+H]⁺, 0.15 min.

Step 2. Preparation of Compound 10

To a solution of Intermediate 1 (289 mg, 0.98 mmol) and Intermediate 7 (200 mg, 0.98 mmol) in dry DMF (10 mL) at 0 C was added DIPEA (0.682 mL, 3.92 mmol) and HATU (447 mg, 1.18 mmol). The resulting mixture was stirred at rt for 1 h. UPLC analysis showed that reaction was complete, water (20 ml) was added and the mixture was extracted with DCM/MeOH 9:1 (2×50 ml). The organic phases were collected together and concentrated. This solid was tritured several times with Et₂O and ACN to afford 91 mg of N-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-2-[3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetamide as white solid. (91 mg, Y=31%).

¹H NMR (400 MHz, DMSO-d6) δ ppm 3.75 (6H, m) 3.89 (4H, m) 6.73 (1H, s) 7.12 (1H, s) 7.69 (3H, d, J=8.8 Hz) 7.87 (2H, d, J=8.6 Hz) 8.20 (2H, br. s.) 8.60 (1H, m) 9.13 (1H, m) 10.35 (1H, m) 12.17 (1H, br. s.) 13.12 (1H, br. s).

LC-MS (Method A): purity: 98% m/z=481.5 [M+H]⁺, 0.45 min.

Example 11 Preparation of 2-[1-methyl-3-(pyridin-3-yl)-1H-pyrazol-5-yl]-N-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}acetamide

Step 1. Preparation of Intermediate 8

Nicotinic acid (6 g, 48.73 mmol), N,O-Dimethylhydroxylamine hydrochloride (4.991 g, 51.17 mmol), HOBt (1.975 g, 14.62 mmol) and A-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (11.21 g, 58.48 mmol) were suspended in ACN (60 mL). NEt₃ (5.128 g, 50.68 mmol, 7 mL) was dropwise added to reaction mixture under N₂ atmosphere. The reaction was stirred at rt overnight.

Water was added and ACN was evaporated under reduced pressure. The aqueous phase was extracted three times with EtOAc. The combined organic phases were washed with H₂O once and, then, with NH₄Cl sat aq (three times), dried over Na₂SO₄ and concentrated under reduced pressure. The crude of reaction was used in the following step without any further purification, (5.1 g, Y=64%).

¹H NMR (400 MHz, DMSO-d6) δ ppm 8.78 (dd, J=2.20, 0.66 Hz, 1H), 8.66-8.70 (m, 1H), 8.00 (dt, J=7.92, 1.98 Hz, 1H), 7.50 (ddd, J=7.92, 4.84, 0.88 Hz, 1H), 3.56 (s, 3H), 3.30 (s, 3H).

LC-MS (Method A): purity: 98% m/z=167.05 [M+H]⁺, 0.34 min.

Sodium hydride (1.20 g, 30.10 mmol, 60% dispersion in mineral oil) was suspended in THF at 0° C. Ethylacetoacetate (3.914 g, 30.10 mmol) was dropwise added at 0° C. (effervescence). The mixture was stirred at 0° C. for 10 minutes (until no effervescence was visible in the flask of reaction) and, then, was cooled to −78° C. n-BuLi (34.61 mmol, 13.84 mL) was dropwise added at −78° C., so that the internal temperature was never higher than −60° C. (time of addition: 10 minutes) and the reaction was stirred at −78° C. for 30 minutes (the mixture turns from light grey to yellowish). Then, N-methoxy-N-methylpyridine-3-carboxamide (5 g, 30.10 mmol) was dropwise added over 10 minutes. The mixture was allowed to warm up to rt and stirred at that temperature overnight. UPLC-MS: reaction completed. Mix was concentrated, HCl aq 0.1 N was added until pH 6 was reached and the mix was extracted with AcOEt (60 ml×2), the organic phases were collected and concentrated. Yellow oil, ethyl 3,5-dioxo-5-(pyridin-3-yl)pentanoate (4.25 g, Y=61%).

Methyl hydrazine (225 mg, 7.01 mmol) and ethyl 3,5-dioxo-5-(pyridin-3-yl)pentanoate (1.5 g, 6.38 mmol) were heated at 70° C. for 5 hours in EtOH (10 mL). Then, the mixture was concentrated under reduced pressure. The crude was purified by RP C-18 column chromatography (H2O/ACN, both with 1% HCOOH=100:00 to 40:60) to give ethyl 2-[1-methyl-3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetate (92 mg Y=5.8%). The structure of the reported isomer was confirmed by NMR studies.

¹H NMR (400 MHz, DMSO-d6) δ ppm 1.23 (3H, t, J=1.2 Hz) 3.81 (3H, s) 3.92 (2H, s) 4.15 (2H, q, J=1.2 Hz) 6.72 (1H, s) 7.41 (1H, dd, J=7.8, 4.8 Hz) 8.10 (1H, dt, J=7.8, 1.8 Hz) 8.16 (1H, s) 8.49 (1H, dd, J=4.8, 1.5 Hz) 8.96 (1H, d, J=1.8 Hz).

LC-MS (Method A): purity: 98% m/z=246.35 [M+H]⁺, 0.43 min.

ethyl 2-[1-methyl-3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetate (92 mg, 0.37 mmol) was dissolved in a mixture of THF/MeOH/H₂O (2.6/0.7/0.7 mL). LiOH (11 mg, 0.38 mmol) was added and the mixture was stirred at room temperature for 1 hour.

The mixture was concentrated under reduced pressure, and the crude of reaction was stripped with a mixture of toluene/MeOH, toluene and DCM to afford 2-[1-methyl-3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetic acid which was used in the following step without any further purification (as Lithium salt), (98 mg, quantitative yield).

¹H NMR (400 MHz, D₂O) δ ppm 3.62 (2H, m) 3.61 (2H, m) 3.76 (3H, m) 6.57 (1H, s) 7.45 (1H, dd, J=8.5, 4.1 Hz) 8.10 (1H, dt, J=8.0, 1.9 Hz) 8.43 (1H, dd, J=5.0, 2.0 Hz) 8.82 (1H, s).

Step 2. Preparation of Compound 11

To a solution of Intermediate 1 (179.04 mg, 0.606 mmol) and 2-[1-methyl-3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetic acid (lithium salt) (98 mg, 0.45 mmol, Intermediate 8) in dry DMF (6.2 mL) at 0° C. was added DIPEA (313.27 mg, 2.42 mmol, 422 μL) and HATU (277 mg, 0.727 mmol). The mixture was stirred at room temperature overnight.

The mixture of reaction was dropwise added to H₂O (30 mL) at rt under stirring. The mixture was stirred at rt for 30 minutes and then, filtered over a Bucher funnel. The solid obtained was taken up in ACN (the product is not soluble in ACN) and few drops of DCM were added. The suspension was stirred at rt for 30 minutes and, then, filtered over a Buchner funnel. The solid on the funnel was washed with a very small amount of ACN, a small amount of Cyclohexane and dried under vacuum over the filter. The solid was collected and dried under vacuum at 50° C. overnight (41 mg, Y=18%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.75 (4H, m) 3.89 (8H, m) 6.74 (1H, s) 7.11 (1H, d, J=2.0 Hz) 7.42 (1H, dd, J=7.9, 4.6 Hz) 7.67 (2H, d, J=8.2 Hz) 7.87 (2H, d, J=8.2 Hz) 8.12 (1H, dt, J=7.0, 2.0 Hz) 8.18 (1H, s) 8.49 (1H, dd, J=4.6, 1.5 Hz) 8.98 (1H, d, J=1.8 Hz) 10.39 (1H, s) 12.17 (1H, br. s)

LC-MS (Method A): purity: 97% m/z=495.4 [M+H]⁺, 0.46 min.

Example 12 Preparation of N-{4-[6-(morpholin-4-yl)-9H-purin-8-yl]phenyl}-2-[3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetamide

Step 1. Preparation of Intermediate 9

6-chloro-9H-purine (1.78 g, 11.5 mmol) was dissolved in ACN (25 ml), the n DIPEA (4.5 g, 34.6 mmol) and Morpholine (3 g, 34.6 mmol) were added, the mixture was warmed to 90° C. (external T) overnight. The mixture was cooled to room temperature and it was added dropwise to Water (90 ml), the slurry was stirred at room temperature for 4 h then the precipitate was recovered by filtration and dried. White solid (1.07 g, Y=63%).

¹H NMR (400 MHz, DMSO-d6) δ ppm 3.73 (4H, m) 4.22 (4H, m) 8.14 (1H, s) 8.23 (1H, s) 13.05 (1H, s).

LC-MS (Method A): purity: 99% m/z=206.26 [M+H]⁺, 0.35 min.

6-(morpholin-4-yl)-9H-purine (1.07 g, 5.2 mmol) was dissolved in ACN (20 ml) then NBS (1.11 g, 6.26 mmol) was added portionwise, the mixture is stirred at 60° C. for 4 h, UPLC-MS reaction completed. The mixture was cooled to room temperature, then it was added dropwise to water (90 ml), the mixture was stirred 1 h at room temperature and filtered. The solid was dried, Pale yellow solid, (1.1 g Y=73%).

¹H NMR (400 MHz, DMSO-d6) δ ppm 3.72 (4H, m) 4.16 (4H, m), 8.24 (1H, s).

LC-MS (Method A): purity: 98% m/z=284.2 and 286.2 [M+H]⁺, 0.55 min.

8-bromo-6-(morpholin-4-yl)-9H-purine (1 g, 3.5 mmol), 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline (1.07 g, 4.9 mmol) and K₃PO₄ (2.23 g, 10.5 mmol) were dissolved in Dioxane/Water (18 ml/6 ml). [1,1′-Bis(diphenylphosphino)ferrocene]dichloropalladium(II) (255 mg, 0.35 mmol) was added and the mixture was heated at 100° C. for 6 h. UPLC analysis showed complete conversion. Water (100 ml) was added and the solid obtained was filtered and washed with 30 ml of diethyl ether to afford of 4-[6-(morpholin-4-yl)-9H-purin-8-yl]aniline. (850 mg, Y=82%), Brown solid.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.75 (4H, m) 4.23 (4H, m) 5.61 (2H, br. s) 6.64 (2H, d, J=8.6 Hz) 7.81 (2H, d, J=8.6 Hz) 8.19 (1H, s) 13.06 (1H, br. s).

LC-MS (Method A): purity: 98% m/z=297.2 [M+H]⁺, 0.50 min.

Step 2. Preparation of Compound 12

To a solution of Intermediate 9 (289.04 mg, 0.98 mmol) and Intermediate 7 (140 mg, 0.98 mmol, Intermediate 8) in dry DMF (6.2 mL) at 0° C. was added DIPEA (682 μL) and HATU (415 mg, 1.09 mmol). The mixture was stirred at room temperature overnight.

The mixture of reaction was dropwise added to H₂O (30 mL) at rt under stirring. The mixture was stirred at rt for 30 minutes and then, filtered over a Bucher funnel. The solid obtained was taken up in ACN. The suspension was stirred at rt for 30 minutes and, then, filtered over a Buchner funnel. The solid on the funnel was washed with a very small amount of ACN, a small amount of cyclohexane and dried under vacuum over the filter. The solid was collected and dried under vacuum at 50° C. overnight. (73 mg, Y=16%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.76 (4H, m) 3.85 (2H, m) 3.85 (2H, s) 4.30 (4H, m) 6.74 (1H, m) 7.45 (2H, m) 7.78 (2H, d, J=8.1 Hz) 8.13 (3H, m) 8.24 (1H, s) 8.51 (1H, br. s) 9.00 (1H, br. s) 10.44 (1H, br. s) 12.94 (1H, m) 13.45 (1H, m).

LC-MS (Method A): purity: 98% m/z=482.2 [M+H]⁺, 0.51 min.

Example 13 Preparation of N-{4-[4-(4-methyl-1H-imidazol-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-2-[3-(pyridin-3-yl)-1H-pyrazol-5-yl]acetamide

Step 1. Preparation of Intermediate 10

4-chloro-6-iodo-7H-pyrrolo[2,3-d]pyrimidine (3 g, 10.7 mmol) was dissolved in DMSO (20 ml) and 4-Methylimidazole (3.5 g, 43 mmol) was added, then TFA (1 g) was slowly added. The mixture was stirred at 150 C for 3 h then was cooled to rt and water (50 ml) was added, the mix is stirred for 30 min at room temperature and filtered. The solid obtained was washed with methanol (2 ml×3 times) to afford 1.1 g of 1-{6-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl}-4-methyl-1H-imidazole. Structure was confirmed by ROESY experiment. Yellow solid (1.1 g, Y=32%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 2.22 (3H, s) 7.33 (1H, s) 7.85 (1H, s) 8.56 (1H, s) 8.59 (1H, s) 13.10 (1H, br. s).

LC-MS (Method A): purity: 95% m/z=326.06 [M+H]⁺, 0.42 min.

1-{6-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl}-4-methyl-1H-imidazole (1 g, 3.1 mmol), 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline (1.07 g, 4.3 mol) and K₃PO₄ (1.97 g, 9.3 mmol) were dissolved in Dioxane/Water (25 ml. 3/1). [1,1′-Bis(diphenylphosphino) ferrocene]dichloropalladium(II) (226 mg, 0.31 mmol) was added and the mixture was heated at 100° C. for 3 h. UPLC analysis showed complete conversion. Water (100 ml) was added and the solid obtained was filtered and washed with 30 ml of diethyl ether to afford 4-[4-(4-methyl-1H-imidazol-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (0.85 g, Y=94%), brown solid.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 2.25 (3H, s) 5.53 (2H, s) 6.66 (2H, d, J=8.6 Hz) 7.22 (1H, s) 7.76 (2H, d, J=8.6 Hz) 7.92 (1H, s) 8.55 (1H, s) 8.65 (1H, s) 12.60 (1H, s).

LC-MS (Method A): purity: 98% m/z=291.2 [M+H]⁺, 0.41 min.

Step 2. Preparation of Compound 13

To a solution of Intermediate 10 (200 mg, 0.69 mmol) and Intermediate 7 (140 mg, 0.98 mmol, Intermediate 8) in dry DMF (6.2 mL) at 0° C. was added DIPEA (682 μL) and HATU (415 mg, 1.09 mmol). The mixture was stirred at room temperature overnight.

The mixture of reaction was purified by RP C-18 column chromatography (H₂O/ACN, both with 1% HCOOH=100:00 to 40:60), The fractions with product were concentrated in order to remove ACN and NH₃ aq 2 M was added until pH 7 was reached, a precipitate was formed. The solid was collected and dried under vacuum at 50° C. overnight. (110 mg, Y=33%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 2.26 (3H, s) 3.86 (2H, m) 6.76 (1H, m) 7.42 (1H, m) 7.50 (1H, s) 7.77 (2H, d, J=7.4 Hz) 7.95 (1H, s) 8.05 (2H, d, J=7.4 Hz) 8.15 (1H, m) 8.51 (1H, br. s) 8.63 (1H, s) 8.69 (1H, d, J=1.1 Hz) 9.00 (1H, br. s) 10.43 (1H, m) 12.98 (1H, br. s).

LC-MS (Method A): purity: 98% m/z=476.2 [M+H]⁺, 0.45 min.

Example 14

Preparation of 1-{4-[5-(morpholin-4-yl)imidazo[1,2-a]pyridin-2-yl]phenyl}-3-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]urea

Step 1. Preparation of Intermediate 11

A 100 mL flask was charged with 6-chloro-2-pyridinamine (2.0 g, 15.56 mmol), 2-bromo-1-(4-nitrophenyl)ethanone (4.2 g, 17.11 mmol) and Methanol (40 mL). The mixture was heated at reflux under stirring over 20 hours. Conversion was monitored over time by UPLC/MS analysis. Formation of a precipitate was observed. After 20 h the mixture was cooled and filtered and the light brown solid was washed with Et₂O (20 mL) to yield target compound 5-chloro-2-(4-nitrophenyl)imidazo[1,2-a]pyridine as light brown powder (precipitate 1). The methanolic filtrate formed more precipitate upon dilution with Et₂O during washings. The suspension was filtered once more, to yield a brown solid which was washed with Et₂O (20 mL) to yield a second fraction of the target compound 5-chloro-2-(4-nitrophenyl)imidazo[1,2-a]pyridine as a dark brown powder (precipitate 2). The two precipitate were mixed together and dried, brown solid (1.48 g, Y=35%).

¹H NMR (400 MHz, DMSO-d₆) δ ppm 7.40 (1H, dd, J=7.4, 0.8 Hz) 7.54 (1H, dd, J=8.9, 7.4 Hz) 7.79 (1H, d, J=9.0 Hz) 8.36 (4H, m) 8.97 (1H, s).

LC-MS (Method A): purity: 92% m/z=274.1 [M+H]⁺, 1.01 min.

In a 20 mL vial to a suspension of 5-chloro-2-(4-nitrophenyl)imidazo[1,2-a]pyridine (600.0 mg, 2.19 mmol) in DMSO (6 mL) was added morpholine (955.02 mg, 10.96 mmol). The vial sealed up and the mixture was heated at 150° C. for 24 hours. UPLC-MS showed conversion by UV>95%. The mixture was cooled, diluted with water (40 mL) and extracted with EtOAc (3×30 mL). The organic layers were collected and concentrated under reduced pressure. The solid obtained was purified by column chromatography (KP-SIL 50 g, gradient EtOAc 10-100% in CycHex) to provide the target compound 4-[2-(4-nitrophenyl)imidazo[1,2-a]pyridin-5-yl]morpholine (236 mg, Y=33.2%) as a yellow solid.

LC-MS (Method A): purity: 95% m/z=325.3 [M+H]⁺, 0.66 min.

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 3.23 (4H, m) 4.03 (4H, m) 6.42 (1H, m) 7.29 (1H, m) 7.47 (1H, d, J=9.0 Hz) 8.00 (1H, m) 8.18 (2H, m) 8.33 (2H, m).

A 50 mL flask equipped with stirring bar and condenser was charged with mixture of 4-[2-(4-nitrophenyl)imidazo[1,2-a]pyridin-5-yl]morpholine (200.0 mg, 0.620 mmol), zinc (241.9 mg, 3.7 mmol), ammonium chloride (197.91 mg, 3.7 mmol) and suspended in a mixture of Ethanol (15 mL) and Water (4 mL) The condenser was filled with nitrogen and the mixture was heated at reflux over 1 hour. UPLC/MS analysis showed the presence of the target product. The resulting mixture was filtered to remove solid and the filtrate was concentrated in vacuo. The residue was partitioned in EtAOc (30 mL) and saturated aqueous sodium bicarbonate solution (30 mL). The aqueous layer was separated and extracted further with EtOAc (2×20 mL), then the organic phases were collected, dried over anhydrous Na₂SO₄ and concentrated in vacuo to give the title compound as a dark yellow solid 4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)aniline (180 mg, Y=98%). The product was proceeded to the following step without further purification.

LC-MS (Method A): purity: 95% m/z=295.3 [M+H]⁺, 0.41 min.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.11 (4H, m) 3.89 (4H, m) 5.21 (2H, s) 6.42 (1H, dd, J=7.0, 1.1 Hz) 6.62 (2H, d, J=1.5 Hz) 7.22 (2H, m) 7.74 (2H, d, J=1.5 Hz) 7.94 (1H, s).

Step 2. Preparation of Compound 14

4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)aniline (40.0 mg, 0.140 mmol) was added to a solution of bis(l-imidazolyl)methanone (44.07 mg, 0.270 mmol) in DCM (4 mL). The mixture was stirred at 25° C. overnight. 3-(pyridin-4-yl)-1H-pyrazol-5-amine (23 mg, 0.14 mmol) was dissolved in DMF (2 mL) and added to the reaction mixture. The mixture was stirred at 60° C. for 6 hours (open vial to evaporate DCM). UPLC/MS showed complete conversion of 3-(pyridin-4-yl)-1H-pyrazol-5-amine and the excess corresponding activated amine. More 3-(pyridin-4-yl)-1H-pyrazol-5-amine (34 mg, 0.230 mmol, 2.5 equiv in total) was added. The mixture was stirred at 60° C. for 1 hour. UPLC/MS showed full conversion of activated 4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)aniline. The mixture was cooled and upon evaporation of most of the DCM, a light brown precipitate was obtained. The mixture was filtered on a phase separator filter and the solid was washed with DCM (3×, 2 mL), MTBE (3×, 2 mL) and Et₂O (3×, 2 mL) to yield pure 1-[4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)phenyl]-3-(3-pyridin-4-yl-1H-pyrazol-5-yl)urea (8 mg, Y=12.3%) as an off-white powder.

LC-MS (Method A): purity: 98% m/z=481.2 [M+H]⁺, 0.49 min.

¹H NMR (400 MHz, DMSO-d₆) δ ppm 3.14 (4H, br. m.) 3.92 (4H, m) 5.99 (1H, s) 6.49 (1H, d, J=6.6 Hz) 6.71 (2H, s) 7.28 (1H, m) 7.35 (1H, m) 7.82 (2H, d, J=8.6 Hz) 7.94 (2H, d, J=6.2 Hz) 8.13 (2H, d, J=8.6 Hz) 8.24 (1H, s) 8.67 (2H, d, J=5.9 Hz) 10.14 (1H, s).

Example 15

Step 1. Preparation of Intermediate 11

3-bromo-1H-pyrazol-5-amine (251 mg, 1.558 mmol), (6-cyanopyridin-3-yl)boronic acid (300 mg, 2.026 mmol), Na₂CO₃ (495.65 mg, 4.676 mmol) were degassed with three cycles of vacuum/N₂, Dioxane (20 mL) and H₂O (2 mL) were added and the mixture was degassed again with 3 cycles of vacuum/N₂. Bis(di-tert-butyl(4-dimethylaminophenyl)phosphine)dichloropalladium(II) (56 mg, 0.0779 mmol) was added to the reaction mixture and the mixture was degassed again with 3 cycles of vacuum and nitrogen. The mixture was heated at 100° C. for 1 hour. The mixture was concentrated and the slurry was purified by RP C-18 column chromatography (H₂O/ACN, both with 1% HCOOH=100:00 to 40:60), The fractions were collected and NH₃ aq 2 M was added until pH 7 was reached, concentrated and stripped 3 times with toluene (15 ml×3) to afford 4-(5-amino-1H-pyrazol-3-yl)pyridine-2-carbonitrile (19 mg Y=6.2%).

LC-MS (Method A): purity: 85% m/z=186.2 [M+H]⁺, 0.44 min.

Step 2. Preparation of Compound 15

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (Intermediate 1, 60 mg, 0.205 mmol) was added to a solution of CDI (70 mg) in DCM (1 ml). The mixture was stirred at rt overnight.

3-[3-(2-cyanopyridin-4-yl)-1H-pyrazol-5-yl]-1-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}urea (19 mg, 0.102 mmol) was dissolved in DMF (0.5 mL) and added to the reaction mixture. The mixture was stirred at 50° C. for 6 hours (open vial to evaporate DCM).

Then, the mixture was cooled to rt and was added to 15 mL of deionized H₂O. The suspension was stirred at rt overnight (greenish-grey sticky solid formation). The suspension was sonicated and filtered over a buchner funnel. The solid was dried under high vacuum and, then, washed with a small amount of EtOAc twice.

The solid was suspended in EtOAC (4 mL) was added. The suspension was sonicated for 30 seconds and centrifuged for 5 minutes (6000 rpm). The solvent was removed and 4 mL of EtOAc were added, the suspension was sonicated 30 seconds and centrifuged for 5 minutes (6000 rpm). The washing with EtOAc was repeated again. The solvent was removed, the solid dried with N₂ first and, then, at 50° C. under high vacuum. (8 mg, Y=15%).

¹H NMR (400 MHz, DMSO-d6) d=12.21 (br. s., 1H), 10.18 (s, 1H), 9.40 (s, 1H), 8.58 (d, J=8.1 Hz, 1H), 8.19 (s, 1H), 7.96 (d, J=8.6 Hz, 1H), 7.81 (d, J=8.6 Hz, 2H), 7.19 (s, 1H), 6.77 (s, 1H), 6.08 (s, 1H), 3.90 (br. s., 4H), 3.85-3.82 (m, 1H), 3.77 (br. s., 4H).

LC-MS (Method A): purity: 95% m/z=507.2 [M+H]⁺, 0.80 min.

Example 16

Step 1. Preparation of Compound 12

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (Intermediate 1, 100 mg, 0.338 mmol) was added to a solution of CDI (77 mg) in DCM (1 ml). The mixture was stirred at rt overnight. 3-(pyridin-4-yl)-1H-pyrazol-5-amine (65 mg, 0.40 mmol) was dissolved in DMF (2 mL) and added to the reaction mixture. The mixture was stirred at 60° C. for 6 hours (open vial to evaporate DCM). UPLC/MS showed full conversion of activated 4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)aniline. The mixture was cooled and upon evaporation of most of the DCM, a light brown precipitate was obtained. The mixture was filtered on a phase separator filter and the solid was washed with DCM (3×2 mL), MTBE (3×2 mL) and Et₂O (3×, 2 mL) to yield pure 1-{4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}-3-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]urea (28 mg, Y=17.2%) as an off-white powder.

¹H NMR (400 MHz, DMSO-d₆) δ 8.57 (s, 1H), 8.17 (s, 1H), 7.83 (d, J=8.8 Hz, 2H), 7.70 (d, J=5.2 Hz, 2H), 7.59 (d, J=8.8 Hz, 2H), 7.06 (s, 1H), 3.94-3.85 (m, 4H), 3.76 (dd, J=5.6, 3.9 Hz, 4H).

LC-MS (Method A): purity: 98% m/z=482.4 [M+H]⁺, 0.48 min.

Example 17

Step 1. Preparation of Intermediate 15

A mixture of 3-bromo-1H-pyrazol-5-amine (375 mg, 3.32 mmol), (2-methylpyridin-4-yl)boronic acid (795 mg, 5.8 mmol), Pd dppf Cl₂ (85 mg, 0.116 mmol), Na₂CO₃ (738 mg, 6.96 mmol), H₂O (1.16 mL) and DME (11 mL) were charged in a microwave vial and degassed for 10 minutes by bubbling N₂ through the mixture. The mixture was heated at 100° C. for 2 days. To the 20 C reaction mixture was added H₂O (150 mL) and the mixture was stirred at rt overnight. The solid was filtered and the aqueous phase was acidified to neutral pH with NH₄Cl aq sat. The aqueous phase was extracted with EtOAc three times, two times again with EtOAc and finally twice with/7-BUOH. The combined organic phases were dried over Na₂SO₄, filtered, evaporated under reduced pressure and purified by flash chromatography using DCM/EtOH as eluent (from 100/0 to 60/40 using a Biotage 25 g KP-Sil column). Fractions with product were collected and concentrated. Yellow solid, 80 mg, 20% yield.

LC-MS (Method A): purity: 100% m/z=175.19 [M+H]⁺, 0.40 min.

¹H NMR (400 MHz, DMSO-d₆) δ 8.39 (d, J=5.2 Hz, 1H), 7.49 (d, J=0.9 Hz, 1H), 7.42 (dd, J=5.4, 1.7 Hz, 1H), 5.85 (br s, 1H), 5.00 (br s, 2H), 2.47 (s, 3H).

Step 2. Preparation of Compound 14

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (intermediate 1, 85 mg, 0.287 mmol) was added to a solution of CDI (79 mg, 0.489 mmol) in DCM. The mixture was stirred at 20° C. overnight. After 14 h other CDI (33 mg, 0.2 mmol) was added and the mixture was stirred at 20 C for 5 hours.

(3-(2-methylpyridin-4-yl)-1H-pyrazol-5-amine (intermediate 15, 63.5 mg, 0.365 mmol) was dissolved in DMF (4 mL) and added to the reaction mixture. The mixture was stirred at 40° C. for 6 hours in a open vial.

Then the mixture was cooled to rt and was added to 150 mL of deionized H₂O. The suspension was stirred at 20 C overnight (greenish-grey sticky solid formation). The suspension was sonicated and filtered over a Buchner funnel. The solid was dried under high vacuum and, then, washed with a small amount of EtOAc twice.

The solid was suspended in 1 mL of DMF and EtOAC (19 mL) was added. The suspension was sonicated for 30 seconds and centrifuged for 5 minutes (6000 rpm). The solvent was removed and 20 mL of EtOAc were added, the suspension was sonicated 30 seconds and centrifuged for 5 minutes (6000 rpm). The washing with only EtOAc was repeated again. The solvent was removed, the solid dried with N₂ first and, then, at 50° C. under high vacuum. 51 mg, 0.103 mmol, 36% Yield, Grey powder.

LC-MS (Method A): purity: 98% m/z=496.31 [M+H]⁺, 0.52 min.

¹H NMR (400 MHz, DMSO-d6) δ=12.21 (s, 1H), 10.11 (s, 1H), 9.00-8.90 (m, 1H), 8.52 (d, J=5.3 Hz, 1H), 8.27-8.13 (m, 1H), 7.95 (d, J=8.6 Hz, 2H), 7.82 (d, J=9.0 Hz, 3H), 7.19 (s, 1H), 6.70 (s, 2H), 5.96 (s, 1H), 3.97-3.85 (m, 4H), 3.82-3.71 (m, 4H), 2.55 (s, 3H).

Example 18

Step 1. Preparation of Intermediate 16

A mixture of 3-bromo-1H-pyrazol-5-amine (375 mg, 3.32 mmol), (2-fluoropyridin-4-yl)boronic acid (821 mg, 5.82 mmol), Pd dppf Cl₂ (85 mg, 0.116 mmol), Na₂CO₃ (738 mg, 6.96 mmol), H₂O (1.16 mL) and DME (11 mL) were charged in a microwave vial and degassed for 10 minutes by bubbling N₂ through the mixture. The mixture was heated at 100° C. for 2 days. To the 20 C reaction mixture was added H₂O (150 mL) and the mixture was stirred at rt overnight. The solid was filtered and the aqueous phase was acidified to neutral pH with HCl 0.5 M aq sol. The aqueous phase was extracted with EtOAc three times, two times again with EtOAc and finally twice with/7-BUOH. The combined organic phases were dried over Na₂SO₄, filtered, evaporated under reduced pressure and purified by flash chromatography using DCM/EtOH as eluent (from 100/0 to 60/40 using a Biotage 25 g KP-Sil column). Fractions with product were collected and concentrated to afford 3-(2-fluoropyridin-4-yl)-1H-pyrazol-5-amine, 65 mg, 16% yield.

LC-MS (Method A): purity: 100% m/z=179.22 [M+H]⁺, 0.48 min

¹H NMR (400 MHz, DMSO-d6) δ ppm 11.92 (br. s., 1H), 11.65 (br. s., 1H), 8.18 (br. s., 1H), 7.61 (d, J=5.06 Hz, 1H), 7.36 (br. s., 1H), 5.87 (br. s., 1H), 5.24 (br. s., 2H).

Step 2. Preparation of Compound 18

4-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]aniline (Intermediate 1, 85 mg, 0.287 mmol) was added to a solution of CDI (79 mg, 0.489 mmol) in DCM. The mixture was stirred at 20 C overnight.

3-(2-fluoropyridin-4-yl)-1H-pyrazol-5-amine (Intermediate 16, 65 mg, 0.365 mmol) was dissolved in DMF (4 mL) and added to the reaction mixture. The mixture was stirred at 40° C. for 6 hours in a open vial.

Then the mixture was cooled to rt and was added to 150 mL of deionized H₂O. The suspension was stirred at 20 C overnight (greenish-grey sticky solid formation). The suspension was sonicated and filtered over a Buchner funnel. The solid was dried under high vacuum and, then, washed with a small amount of EtOAc twice.

The solid was suspended in 1 mL of DMF and EtOAC (19 mL) was added. The suspension was sonicated for 30 seconds and centrifuged for 5 minutes (6000 rpm). The solvent was removed and 20 mL of EtOAc were added, the suspension was sonicated 30 seconds and centrifuged for 5 minutes (6000 rpm). The washing with only EtOAc was repeated again. The solvent was removed, the solid dried with N₂ first and, then, at 50° C. under high vacuum. 41 mg, 0.103 mmol, 28% Yield, Grey powder.

LC-MS (Method A): purity: 97% m/z=500.29 [M+H]⁺, 0.80 min. ¹H NMR (400 MHz, DMSO-d₆) δ 12.21 (s, 1H), 10.17 (s, 1H), 8.33 (d, J=5.2 Hz, 1H), 8.20 (s, 1H), 7.96 (d, J=8.7 Hz, 2H), 7.91 (d, J=4.7 Hz, 1H), 7.82 (s, 1H), 7.79 (d, J=7.2 Hz, 2H), 7.19 (s, 1H), 6.75 (s, 2H), 6.05 (s, 1H), 3.90 (d, J=5.1 Hz, 5H), 3.77 (t, J=4.9 Hz, 5H).

Example 19

Step 1. Preparation of Compound 19

4-[4-(morpholin-4-yl)-1H-imidazo[4,5-c]pyridin-2-yl]aniline (Intermediate 14, 125.0 mg, 0.340 mmol) was suspended in DCM (7 mL), CDI (219.61 mg, 1.35 mmol) was added and the mixture was stirred at rt for 10 hours. Once the activation was completed (check by UPLC with MeOH quenching) 3-pyridin-3-yl-1h-pyrazol-5-amine (54.24 mg, 0.340 mmol) was added, followed by DMF (5 mL). The mixture was stirred at 40° C. for 4 hours in an open vial. The mix was cooled to 20° C. then H₂O (6 ml) was added to the reaction mixture. The sticky solid obtained after filtration was washed 4 times with H2O (3 ml). Then it was centrifuged using EtOAc as solvent 4 times and, finally, was purified by reverse phase flash chromatography (KP-C18 12 g, H₂O-CAN 100:00 to 60:40) to yield pure 1-{4-[4-(morpholin-4-yl)-1H-imidazo[4,5-c]pyridin-2-yl]phenyl}-3-[3-(pyridin-3-yl)-1Hpyrazol-5-yl]urea, 11 mg, 6.7% Yield as an off-white powder.

¹H NMR (400 MHz, DMSO-J6) 6 ppm 13.05 (br. s., 1H), 10.22 (s, 1H), 9.20 (d, J=1.76 Hz, 1H), 8.61 (dd, J=4.84, 1.32 Hz, 1H), 8.33 (dt, J=8.14, 1.87 Hz, 1H), 8.14 (d, J=8.36 Hz, 2H), 7.93 (d, J=8.80 Hz, 2H), 7.83 (d, J=5.72 Hz, 1H), 7.50 (dd, J=7.70, 5.06 Hz, 1H), 6.92 (d, J=5.72 Hz, 1H), 6.71 (s, 2H), 5.96 (s, 1H), 4.06-4.13 (m, 4H), 3.77-3.81 (m, 4H).

LC-MS (Method A): purity: 96% m/z=482.2 [M+H]⁺, 0.54 min.

Example 20

Step 1. Preparation of Compound 20

4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)aniline (Intermediate 11, 70.0 mg, 0.240 mmol) was added to a solution of CDI (57.84 mg, 0.360 mmol) in DCM (10 mL). The mixture was stirred at 25° C. overnight. 3—Pyridin-3-yl-1h-pyrazol-5-amine (40.0 mg, 0.250 mmol) was dissolved in DMF (5 mL) and added to the reaction mixture. The mixture was stirred at 50° C. for 6 hours (open vial to evaporate DCM). Then, the mixture was cooled to 20 C, concentrated under reduced pressure, and the crude was purified by column chromatography (KP—NH-SiCh, gradient MeOH 0-10% in DCM) to yield a light yellow powder with ca. 90% purity. The obtained solid (ca. 30 mg) was triturated with MTBE (3×3 mL) to yield pure 1-[4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)phenyl]-3-(3-pyridin-3-yl-1H-pyrazol-5-yl)urea (20 mg, 0.042 mmol, 17.5% yield) as an off-white powder.

LC-MS (Method A): purity: 99% m/z=481.3 [M+H]⁺, 0.55 min.

¹H NMR (400 MHz, Chloroform-d) δ 9.28 (s, 1H), 9.06 (dd, J=2.2, 0.9 Hz, 1H), 8.65 (dd, J=4.8, 1.7 Hz, 1H), 8.15 (dt, J=7.9, 1.9 Hz, 1H), 8.05 (d, J=8.6 Hz, 2H), 7.86 (s, 1H), 7.73 (d, J=8.7 Hz, 2H), 7.46 (d, J=9.0 Hz, 1H), 7.40 (ddd, J=8.0, 4.8, 0.9 Hz, 1H), 7.24 (dd, J=9.0, 7.2 Hz, 1H), 6.37 (dd, J=7.3, 0.9 Hz, 1H), 5.85 (s, 1H), 5.66 (s, 2H), 4.07-3.99 (m, 4H), 3.20 (m, J=4.5 Hz, 4H).

Example 21

Step 1. Preparation of Compound 21

A 5 mL microwave tube equipped with magnetic stirrer was charged with 4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)aniline (Intermediate 11, 40.0 mg, 0.140 mmol) CDI (24.2 mg, 0.150 mmol). DCM (3 mL) was added and the mixture was stirred at 25° C. over 4 h. UPLC/MS analysis of the reaction mixture upon quenching with MeOH allowed monitoring of the conversion. More CDI (0.6 equiv, 15 mg) was added to the reaction mixture and stirred over 1 h. UPLC (quench with MeOH) showed reaction completion. 2-(5-amino-1H-pyrazol-3-yl)propan-2-ol (23.02 mg, 0.160 mmol) was dissolved in DMF (1 mL) and added to the reaction mixture. The mixture was stirred at 60° C. for 16 hours (open vial to evaporate DCM). The residual DCM was evaporated and the residual solution in DMF was diluted by dropwise addition of water (2 mL) to force precipitation. The obtained slurry was stirred over 1 h, then filtered on a phase filter and washed with water (3×, 3 mL).

The solid was purified by column chromatography (SiO₂, gradient MeOH 0-20%, 20 CV) to yield the pure target compound 1-[3-(2-hydroxypropan-2-yl)-1H-pyrazol-5-yl]-3-[4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)phenyl]urea (2.6 mg, 0.006 mmol, 4.146% yield) as a beige amorphous solid. UPLC/MS and MNR analysis of confirmed the expected structure. Similarly, the liquid fraction was purified by column chromatography (SiO₂, gradient MeOH 0-20%, 20 CV) to yield the pure target compound 1-[3-(2-hydroxypropan-2-yl)-1H-pyrazol-5-yl]-3-[4-(5-morpholin-4-ylimidazo[1,2-a]pyridin-2-yl)phenyl]urea (21 mg, 0.0455 mmol, 30% yield) as a beige amorphous solid.

LC-MS (Method A): purity: 99% m/z=462.3 [M+H]⁺, 0.52 min.

¹H NMR (400 MHz, Methanol-d4) δ 8.05 (s, 1H), 7.95 (d, J=8.7 Hz, 2H), 7.59 (d, J=8.7 Hz, 2H), 7.39-7.32 (m, 2H), 6.55 (dd, J=6.2, 2.0 Hz, 1H), 6.12 (s, 1H), 4.05-3.96 (m, 4H), 3.24-3.18 (m, 4H), 1.58 (s, 6H).

Example 22 (Compound 26)

Step 1. Preparation of Compound 26

4-(4-methyl-1H-imidazo[4,5-c]pyridin-2-yl)aniline (Intermediate 24, 80.0 mg, 0.36 mmol) and 5-isocyanato-3-pyridin-4-yl-1,2-oxazole hydrochloride (Intermediate 5, 96 mg, 0.43 mmol) were added to a 25 ml round bottom flask, then DMSO (2 mL) and triethylamine (160 ul) were added, the mixture was stirred 6 h at 20° C. UPLC-MS: reaction completed (check UPLC) and water (20 ml) was added, the precipitate was collected and washed with water (20 ml) and Et₂O (30 ml), pale green solid. The solid was collected and suspended in MeOH, active carbon was added (50 mg), the mixture was heated to 50° C. for 20 min, cooled and filtered. Filtrate was concentrated to afford 1-[4-(4-methyl-1Himidazo[4,5-c]55pyridine-2-yl)phenyl]-3-(3-pyridin-4-yl-1,2-oxazol-5-yl)urea, 49 mg, 33% yield.

LC-MS (Method A): purity: 99% m/z=412.2 [M+H]⁺, 0.44 min

¹H NMR (400 MHz, Methanol-d4) δ 8.73-8.69 (m, 2H), 8.21-8.15 (m, 3H), 7.92-7.87 (m, 2H), 7.77 (d, J=8.9 Hz, 2H), 7.52 (d, J=5.9 Hz, 1H), 6.76 (s, 1H), 2.89 (s, 3H). 4H), 1.58 (s, 6H).

Example 23 (Compound 31)

Step 1. Preparation of Intermediate

4-nitrobenzoic acid (5.82 g, 34.83 mmol), DIPEA (6.07 mL, 34.83 mmol) and HATU (13 g, 34.83 mmol) were dissolved in DMF (75 mL) and stirred at 20 C for 20 minutes. In another vial 2-chloropyridine-3,4-diamine (5 g, 34.83 mmol) was dissolved in DMF (125 mL). The solution containing the activated acid was dropwise added to the solution of the amine. The reaction was stirred at 20 C overnight. H₂O (250 ml) was added and the solid obtained was filtered, washed with H₂O and a small amount of Et₂O, the solid was dried at 50 C under vacuum to afford N-(4-amino-2-chloropyridin-3-yl)-4-nitrobenzamide, 5.09 g, 50% yield.

LC-MS (Method A): purity: 70% m/z=292.1 [M+H]⁺, 0.53 min.

A 50 mL round bottom flask equipped with stirring bar and reflux condenser was charged with N-(4-amino-2-chloropyridin-3-yl)-4-nitrobenzamide (8.0 g, 27.33 mmol) and Phosphorus(V) oxychloride (20.44 mL, 218.67 mmol). The mixture was heated at 110° C. over 6 h. Conversion was monitored by UPLC/MS analysis. The mixture was cooled at RT, then added to 300 mL of ice-water mixture and solid NaHCO₃ was added under stirring until neutral pH was reached. The mixture was transferred in a separator funnel and extracted with EtOAc (3×, 200 mL). A thick foam layer was observed in the organic-aqueous interphase in each case. This foam layer was filtered on a phase separator cartridge to remove the insoluble solid. The collected organic phases were dried over Na₂SO₄ and concentrated under reduced pressure. The residue was purified by column chromatography (SiO₂, EtOAc in Cyclohexane from 50% to 100% to afford 4-chloro-2-(4-nitrophenyl)-3H-imidazo[4,5-c]pyridine 3.2 g 45% yield, yellow solid.

LC-MS (Method A): purity: 75% m/z=275.2 [M+H]⁺, 0.82 min.

A 20 mL microware vial equipped with stirring bar was charged with 4-chloro-2-(4-nitrophenyl)-1H-imidazo[4,5-c]pyridine (0.75 g, 1.91 mmol), 4-methyl-1H-imidazole (1.26 g, 15.29 mmol) and DMSO (5 mL). Trifluoroacetic acid (0.22 mL, 2.87 mmol) was added and the mixture was degassed with 3 vacuum/nitrogen back-filling cycles. The mixture was heated at 140° C. over 1 h in a microwave reactor. UPLC/MS analysis showed appearance of the target compound (0.58 min, m/z+=321, 20% conversion by UV abs). The mixture was heated further at 150° C. over 2 h. UPLC/MS analysis showed higher conversion (ca. 70% conversion by UV abs). The mixture was cooled and partitioned between EtOAc (100 mL) and water (100 mL). The organic phase was washed with water (3×, 100 mL) and brine, filtered on a phase separator, dried over Na₂SO₄ and concentrated under reduced pressure. The residue was purified by column chromatography (SiO₂, gradient MeOH 0-10% in DCM) to yield the target product 4-(4-methylimidazol-1-yl)-2-(4-nitrophenyl)-1H-imidazo[4,5-c]pyridine (80 mg, 0.250 mmol, 13% yield).

LC-MS (Method A): purity: 94% m/z=321.4 [M+H]⁺, 0.58 min.

¹H NMR (400 MHz, DMSO-d6) δ 9.08 (d, J=1.3 Hz, 1H), 8.56 (d, J=9.0 Hz, 2H), 8.47 (d, J=9.0 Hz, 2H), 8.21 (d, J=5.5 Hz, 1H), 8.18 (s, 1H), 7.57 (d, J=5.6 Hz, 1H), 2.26 (d, J=1.1 Hz, 3H).

A 100 mL hydrogenation round bottom flask was equipped with a stirring bar and charged with 4-(4-methylimidazol-1-yl)-2-(4-nitrophenyl)-1H-imidazo[4,5-c]pyridine (80.0 mg, 0.250 mmol), Ethanol (10 mL) and palladium on carbon 10 w % (26.58 mg, 0.020 mmol). The flask was filled with hydrogen (atm. press) and let to stir at RT over 24 h. UPLC/MS analysis) showed incomplete conversion, due to poor dissolution of substrate in EtOH. DMF (5 mL) was added, but solubility did not improve. HCl (aq. 37%, 0.05 mL) was added to the suspension, resulting in rapid dissolution of flocculant. The hydrogenation was continued at RT for 4 h. UPLC/MS analysis showed complete conversion of starting nitro-derivative. The mixture was filtered on a plug of celite, washed with EtOAc and concentrated under reduced pressure. A dark yellow precipitate formed over time from the residual DMF. The DMF was removed with a V10 high vacuum pump, yielding the chloridrate salt of target compound as a brown solid 4-[4-(4-methylimidazol-1-yl)-1H-imidazo[4,5-c]pyridin-2-yl]aniline (135 mg, 0.465 mmol, 186.18% yield). MeOH (20 mL) and DCM (20 mL) was added to the residue to obtain a yellow suspension and NH₃ 7 M in MeOH (0.1 mL) was added to neutralize the residual acid. The volatiles were removed at reduced pressure. The solid residue was triturated in water (15 mL) and the slurry was filtered. The brown solid was washed with water (3×, 2 mL) and MTBE (3×, 1 mL) and dried under suction. The product 4-[4-(4-methylimidazol-1-yl)-1H-imidazo[4,5-c]pyridin-2-yl]aniline (35 mg, 0.121 mmol, 48.3% yield) was recovered as a brown powder.

LC-MS (Method A): purity: 88% m/z=291.4 [M+H]⁺, 0.43 min. ¹H NMR (400 MHz, DMSO-d6) δ 13.20 (s, 1H), 9.11 (s, 1H), 8.18 (s, 1H), 8.10 (d, J=5.5 Hz, 1H), 7.95 (d, J=8.3 Hz, 2H), 7.42 (d, J=5.5 Hz, 1H), 6.72 (d, J=8.3 Hz, 2H), 2.26 (s, 3H).

Step 2. Preparation of Compound 31

4-[4-(4-methylimidazol-1-yl)-1H-imidazo[4,5-c]pyridin-2-yl]aniline (Intermediate 22 35.0 mg, 0.120 mmol), 2-(3-pyridin-3-yl-1H-pyrazol-5-yl)acetic acid (Intermediate 7, 29.4 mg, 0.140 mmol) were dissolved in DMF (3 mL). N,N-Diisopropylethylamine (0.02 mL, 0.120 mmol) was added and the mixture was cooled at 0° C. [dimethylamino(3-triazolo[4,5-b]pyridinyloxy)methylidene]-dimethylammonium;hexafluorophosphate (59.59 mg, 0.160 mmol) was added to the mixture. The solution was stirred at 0° C. for 30 minutes and 1 hour at 25° C. UPLC analysis showed incomplete conversion. More 2-(3-pyridin-3-yl-1H-pyrazol-5-yl)acetic acid (Intermediate 7, 29.4 mg, 0.140 mmol), N,N-Diisopropylethylamine (0.02 mL, 0.120 mmol), and [dimethylamino(3-triazolo[4,5-b]pyridinyloxy)methylidene]-dimethylammonium; hexafluorophosphate (59.59 mg, 0.160 mmol) were added. The reaction mixture was stirred at 20° C. over night. UPLC: reaction completed. Work Up: H₂O (15 ml) was added and the suspension was stirred at rt for 1 h. the slurry was centrifuged and the solid was washed with water, filtered over buchner, washed with water and MTBE to give a dark brown solid (50 mg). UPLC and NMR analysis showed the target product with various impurities. The solid residue was triturated with water (2×, 20 mL) and centrifuged. The solid was then purified by reverse flash column chromatography (C18-functionalized SiO₂, gradient ACN 0-40% in aq. 0.1% HCOOH) to afford the target compound, which were collected and lyophilized. The target product N-[4-[4-(4-methylimidazol-1-yl)-1H-imidazo[4,5-c]pyridin-2-yl]phenyl]-2-(3-pyridin-3-yl-1H-pyrazol-5-yl)acetamide (4 mg, 0.008 mmol, 6.9% yield) was obtained as a light brown solid.

LC-MS (Method A): purity: 93% m/z=476.1 [M+H]⁺, 0.72 min.

¹H NMR (400 MHz, Methanol-d4) δ 9.21 (s, 1H), 8.97 (s, 1H), 8.51 (d, J=5.2 Hz, 1H), 8.42 (s, 1H), 8.25-8.16 (m, 5H), 7.87 (d, J=8.5 Hz, 2H), 7.55-7.46 (m, 3H), 6.78 (s, 1H), 3.92 (s, 2H), 2.37-2.32 (m, 3H).

Example 24 (Compound 35)

Step 1. Preparation of Compound 35

4-(4-morpholin-4-yl-1H-imidazo[4,5-c]pyridin-2-yl)aniline (Intermediate 14, 10.0 mg, 0.030 mmol), 2-[3-(5-fluoropyridin-3-yl)-1H-pyrazol-5-yl]acetic acid (Intermediate 25, 9 mg, 0.040 mmol) were dissolved in DMF (2 mL). N,N-Diisopropylethylamine (4.38 mg, 0.030 mmol) was added and the mixture was cooled at 0° C. [dimethylamino(3-triazolo[4,5-b]pyridinyloxy)methylidene]-dimethylammonium;hexafluorophosphate (38.62 mg, 0.100 mmol) was added to the mixture. The solution was stirred at 0° C. for 30 minutes and 1 hour at 25° C. UPLC analysis showed complete conversion. The reaction mixture was stirred at rt over night. The mixture was concentrated under reduced pressure, the residue was then purified by reverse flash column chromatography (KP-C18, gradient ACN 1-25% in aq. 0.1% HCOOH) to afford a purified fraction of the target compound, which were collected and lyophilized to yield the target compound 2-[3-(5-fluoropyridin-3-yl)-1H-pyrazol-5-yl]-N-[4-(4-morpholin-4-yl-1H-imidazo[4,5-c]pyridin-2-yl)phenyl]acetamide (4 mg, 0.008 mmol, 23.7% yield) as an off-white sponge.

LC-MS (Method B): purity: 98% m/z=499.2 [M+H]⁺, 0.74 min.

¹H NMR (400 MHz, Methanol-d4) δ 8.85 (s, 1H), 8.43 (s, 1H), 8.30 (s, 1H), 8.09 (d, J=8.8 Hz, 2H), 8.02 (d, J=9.9 Hz, 1H), 7.82 (d, J=8.8 Hz, 2H), 7.78 (d, J=6.2 Hz, 1H), 7.08 (d, J=6.2 Hz, 1H), 6.80 (s, 1H), 4.17 (s, 4H), 3.97-3.91 (m, 6H).

Example 25 (Compound 36)

Step 1. Preparation of Compound 36

A 5 mL tube equipped with stirring bar was charged with a solution CDI (44 mg, 0.270 mmol) in DCM (3 mL). 4-(4-morpholin-4-yl-1H-imidazo[4,5-c]pyridin-2-yl)aniline (Intermediate 14, 54.0 mg, 0.180 mmol) added to the solution. The slurry was stirred at RT over 16 h. UPLC/Ms analysis showed complete conversion. 2-(5-amino-1H-pyrazol-3-yl)propan-2-ol (Intermediate 21, 28 mg, 0.200 mmol) was dissolved in a mixture of DCM (1.5 mL)—DMF (0.200 mL) and added to the slurry. The mixture was heated at 60° C. and the volatiles were evaporated over night. After removal of the residual DCM, the slurry was diluted with water (4 mL) causing precipitation of a white solid. The slurry was filtered on a phase separator cartridge and washed with water (4×1 mL) to wash off the residual DMF. The solid was purified by column chromatography (SiO₂, gradient MeOH 0-40% in DCM) to yield the target compound 1-[3-(2-hydroxypropan-2-yl)-1H-pyrazol-5-yl]-3-[4-(4-morpholin-4-yl-1H-imidazo[4,5-c]pyridin-2-yl)phenyl]urea (23 mg, 0.050 mmol, 27.2% yield) as a light brown powder.

LC-MS (Method A): purity: 95% m/z=463.5 [M+H]⁺, 0.58 min.

¹H NMR (400 MHz, DMSO-d6) δ 13.02 (s, 1H), 9.83 (s, 1H), 8.11 (d, J=8.7 Hz, 2H), 7.90-7.78 (m, 3H), 6.91 (d, J=5.6 Hz, 1H), 6.43 (s, 2H), 5.40 (s, 1H), 4.94 (s, 1H), 4.09 (t, J=4.9 Hz, 4H), 3.78 (t, J=4.8 Hz, 4H), 1.44 (s, 6H).

Additional Exemplary Compounds of the Invention

Other compounds of the invention have been or can be prepared according to the synthetic methods, or some variations thereof, described herein. The compounds can be prepared from readily available starting materials using the following general methods and procedures. It will be appreciated that where typical or preferred process conditions (i.e., reaction temperatures, times, mole ratios of reactants, solvents, pressures, etc.) are given; other process conditions can also be used unless otherwise stated. Optimum reaction conditions may vary with the particular reactants or solvent used, but such conditions can be determined by one skilled in the art by routine optimization procedures.

The following compounds prepared or can be prepared from readily available starting materials using the general methods and procedures described herein are depicted in Table 1:

TABLE 1 Representative compounds of the invention Pat ID Structure MW 1

491.50 2

482.49 3

467.49 4

437.46 5

481.51 6

538.60 7

538.60 8

482.49 9

481.51 10

480.52 11

495.54 12

480.52 13

475.50 14

480.52 15

506.52 16

481.51 17

495.54 18

499.50 19

481.52 20

480.53 21

461.53 22

482.51 23

482.51 24

481.52 25

468.53 26

411.42 27

550.63 28

539.64 29

553.64 30

411.42 31

475.52 32

494.56 33

475.52 34

462.51 35

498.52 36

462.21

The following additional compounds are or can be prepared from readily available starting materials using the following general methods and procedures:

Example 101a: Menin-MLL In Vitro Inhibitory Activity

The menin-MLL IC₅₀s of compounds disclosed herein is determined as described below.

Cell Preparation:

The MLL-rearranged MOLM13 cell line and the MLL-germline cell line HL60 growing in log phase cultures was counted and re-suspended at a concentration of 10,000 cells/100 ul (100,000 cells/ml) in RPMI 10% FBS containing medium with Pen/Strep.

A total of 100 uls were plated in each well of a round-bottom 96 well non-tissue treated plate (Corning). Thus, each well had 10,000 MOLM13 or HL60 cells on day.

Compound Dilution:

Each compound was diluted to a final concentration of 5 mM in DMSO. 15 ml Falcon tubes were used for making the dilution. These 5 mM stocks were stored in 2 ml light-protective Eppendorf tubes in multiple 50 ul aliquots to prevent repeated freeze-thaw of the entire stock.

The following concentrations were decided for each compound: 0.01 μM, 0.03 μM, 0.1 μM, 0.3 μM, 0.5 μM, 1 μM, 3 μM, and 5 μM.

First, 2× working stocks for each desired concentration were made using the standard RPMI 10% FBS medium as the diluent.

Specifically, working stocks of 0.02 μM, 0.06 μM, 0.2 μM, 0.6 μM, 1 μM, 2 μM, 6 μM and 10 μM (2× of the desired concentrations mentioned above) were made from the 5 mM stock (see note at the bottom for more details).

100 μl of each working stock dilution was added to the respective well containing 100 μl of plated cells, thereby achieving a 1× drug concentration. A similar strategy was used for the DMSO control arm.

Proliferation Assays:

Proliferation is measured using the BD Fortes' flow cytometry machine and FACS Diva software. Total numbers of live cells are measured by staining cells with a dead cell stain such as Sytox. Cells are re-planted every 3-4 days and counting is performed on days 3, 7 and 10 or 3, 6 and 9. Differentiation of cells is measured using CD11b as a marker of monocytic differentiation.

Note:

To minimize inaccuracies, once a stock of higher concentration was made, 10 fold dilutions were made from that working stock. Eg: first the 10 μM 2× working stock was made by adding 4 μM of the 5 mM drug to 2 mL of medium. From this, the 1 μM and 0.1 working stocks were made by vortexing the 10 μM stock vigorously and adding 90 μL of this to 810 μL of medium (1:10 dilution). Subsequently, a similar 1:10 dilution of the 1 μM stock (90 μL, 1 μM stock+810 μL medium) gave a 0.1 μM working stock. In this way, 2× working stocks of 0.02 μM, 0.06 μM, 0.1 μM, 0.2 μM, 0.6 μM, 1 μM, 2 μM and 10 μM were made.

The IC₅₀s menin-MLL inhibition are determined using methods known to one skilled in the art.

TABLE 2 IC₅₀ Values for Exemplary Compounds of the Invention Compound Menin-MLL ID Name IC₅₀ nM 2 1-(4-(4-morpholino-7H-pyrrolo 240 [2,3-d]pyrimidin-6-yl)phenyl)-3-(3- (pyridin-3-yl)isoxazol-5-yl)urea

Example 5b: IC₅₀ Determination of Compounds of Invention in Various Cell Lines (Long Term Proliferation Assay)

Cell Lines

The following 5 cell lines are used or can be used for the long term proliferation assay.

Cell Line Source Cat # Description MLL-rearrangement RS4;11 ATCC CRL-1873 leukemia, acute lymphoblastic MLL-AF4 NOMO-1 JCRB IFO50474 leukemia, acute monocytic MLL-AF9 leukemia HL-60 ATCC CCL-240 leukemia, acute promyelocytic MV-4-11 ATCC CRL-9591 leukemia, biphenotypic B MLL-AF4 myelomonocytic Molm-13 AddexBio C0003003 leukemia, acute, myeloid, MLL-AF9 leukemia suspension

TABLE 3A IC₅₀ Values for Exemplary Compounds of the Invention MV-4-11 MOLM-13 Day 4 Day 11 Day 4 Day 11 Pat IC₅₀ IC₅₀ IC₅₀ IC₅₀ Kd ID (nM) (nM) (nM) (nM) (μM)  2 174  55  74  54 (>) >1  5 129  66 115  32  6 229  74 178  50  7 891  631 933 871  8 355  71 224  55 0.25  9 490  257 324 155  1.2 ± 0.5/ 1.6 ± 0.8 10 220  310 2.7 ± 4   11 280  260 1.7 ± 1.8 12 430  710 0.5 ± 0.2 13 910 1230 1.6 ± 1.8

TABLE 3B Additional IC₅₀ Values for Exemplary Compounds of the Invention (Cell Titer-Glo) Day 4 Day 7 Day 11 Day 14 Pat Cell IC₅₀ IC₅₀ IC₅₀ IC₅₀ ID Type (nM) (nM) (nM) (nM) 8 KG-1 4900 2950 2140  680 MOLM-13  320  200  150  250 OCI-AML-3  590  560  550  550 MV4-11  540  100  200  60 9 KG-1 >5000  4790 1700 1230 MOLM-13  410  240  240  480 OCI-AML-3  870  710  650  720 MV4-11  740  380  320  210

TABLE 3C Additional IC₅₀ Values for Exemplary Compounds of the Invention (InCell) Day 4 Day 11 Pat Cell IC₅₀ IC₅₀ ID Type (nM) (nM) 8 KG-1 3240 2090 MOLM-13  370  190 OCI-AML-3  490  540 MV4-11  350  280 9 KG-1 3310 2290 MOLM-13  520  340 OCI-AML-3  370  720 MV4-11  500  430 Long Term Proliferation Assay Design

Compounds of invention are tested in the 5 suspension lines by 14-day long-term proliferation assay.

The compound is tested in 10-pt dose titration (client will determine the starting concentration and the dilution scheme) and the final DMSO concentration is kept at 0.2%.

Vehicle and media control are also included. All treatments are done in triplicate.

3 plates are used for each cell line and 15 plates are used for the 5 cell lines.

Long Term Proliferation Assay Protocol

-   -   1) On Day 0, in a flat bottom 96-well plate, add 100 μL of cells         per well at the densities optimized.     -   2) Prepare compounds in DMSO at 500× final concentration. Dilute         the compounds with DMSO at the dilution.     -   3) Dilute the compounds in media at 3× final concentration. Add         50 μL of compound or DMSO at 3× final concentration to each         well. Final volume in each well is 150 μL, and final         concentration of DMSO is 0.2%. Also include 3 untreated control         wells, by adding 50 μL of media alone.     -   4) Incubate plates for 96 hours.     -   5) Count the cells using the Acumen, with capabilities for         96-well plates. Pipette cells up and down to mix in each well,         and add desired volume of cells to a new flat bottom         poly-D-lysine 96-well plate. Add Calcein AM at 1 μM final         concentration. Let cells sit at RT for 10 mins followed by a         quick spin to get cells settled on the bottom of the wells.         Incubate the plate for additional 40 mins in the incubator. Take         out the plate and read by Acumen. Calculate the cell numbers         taken into account the dilution factors.     -   6) Split the master plate. To do this take the total viable cell         count calculated using step 5). Take the average of the         replicates for each dose in order to be used in splitting the         cells.     -   7) Use a 96 well V-bottom plate to spin down the cells to remove         old media and compound to split the cells. Based on the split         ratio place the proper amount of media and cells into the         V-bottom plate, and spin the plate at 1100 rpm for 5 minutes.     -   8) Following the spin remove the media, careful not to disturb         the cell pellet.     -   9) Re-suspend pellet in 100 μL fresh media, and add to a new         96-well flat bottom plate.     -   10) Add fresh compound, in the same manner as Step 3).     -   11) Incubate plates for 72 hours. Repeat steps 5)-10) on Day 7.     -   12) Incubate plates for 96 hours. Repeat Step 5)-10) on Day 11.     -   13) Incubate 72 hours and repeat step 5) to take a final count.     -   14) Data Analysis

To calculate growth for days 4, 7, 11, and 14:

-   -   Calculate the split factor for day 4 to 7, day 7 to 11, and day         11-14. The split factor is the viable cells/mL on Day X (either         4, 7 or 11) divided by the density the cells are being split         back to.     -   For growth of cells from day 4 to 7, multiply the day 7 viable         cells/mL density by the split factor from day 4.     -   For growth of cells from day 7 to 11, multiply the day 11 viable         cells/mL density by the days 4, and 7 split factors.     -   For growth of cells from Day 11 to 14, multiply the Day 14         viable cells/mL density by the days 4, 7, and 11 split factors.     -   Plot growth on semi-log chart (viable cells/mL on Y axis, in         log, and days on X axis).     -   The growth inhibition was calculated with the formula         ((untreated cell numbers−treated cell numbers)/untreated         cell))).     -   Calculate the IC50 for each compound in each line using XLFit         (Sigmoidal Dose-Response Model,         y=(Bottom+((Top-Bottom)/(l+((IC50/x){circumflex over         ( )}Hill))))).         Results:

The IC₅₀ graphs of menin-MLL inhibition for Compound 2 in various cell lines along with the comparison with a known menin-MLL inhibitor MI-503 (Borkin et al. 2015, Cancer Cell 27, 589-602) are depicted in FIGS. 1-4 .

Example 102: Proliferation Study in MLL-Leukemia Cells

Introduction and Rationale

The objective of the study was to evaluate the ability of representative compounds of the present invention, inhibitors of Menin/MLL interaction to inhibit cell proliferation. The proliferation inhibitory effect was investigated in two human MLL-leukemia cells selected on the bases of MLL fusion protein and listed in Table 102. HL-60 cell line was used as negative control.

TABLE 102 Human MLL-leukemia cells Cell Type MLL gene fusion MV-4-11 MLL-AF4 MOLM-13 MLL-AF9

ATP is present in all metabolically active cells and is considered as a marker for cell viability and proliferation. The metabolic cell activity was determined using the CellTiter-Glo kit from Promega, an ATP monitoring system based on the production of luminescence by the reaction of ATP with added UltraGlo® recombinant luciferase (Kawano et al., 2016), according to the supplier's experimental recommendations.

Experimental Design

The described assay evaluates the ability of 4 representative compounds to inhibit the cell proliferation in the human MLL-leukemia cells plus a negative control cell line.

The assay provides potency values (IC₅₀) for each test compound at a single time point Day 4 (T4).

Seven concentrations of the compounds (2.00E-05-6.67E-06-2.22E-06-7.41E-07-2.47E-07-8.23E-08-2.74E-08M), were assessed in duplicate in an individual test occasion in all the cell lines. MI-503 (Borkin et al., 2015) was used as reference compound and was tested at the same concentrations as the NCEs. 100% of proliferation is represented by the untreated cells (0.2% DMSO). The cell growth was monitored up to 4 days in culture.

Materials and Methods

Cell Culture

MV4-11, MOLM-13 and HL-60 cells (see Table 2) were maintained in RPMI-1640 medium (Invitrogen, Cat. n. 618700, Batch n. 1965930) supplemented with 10% of Heat Inactivated FBS (Invitrogen, Cat n. 10500, Batch n. 08Q8078K) and 1% Pen-Strep (Invitrogen, Cat. N. 15140, Batch n. 1910859) and cultured at 37° C. in a humidified incubator with 5% CO2. All the cell lines grow in suspension and the cell density was maintained in a range of 2×10⁵-1×10⁶ viable cells/ml. Cells were pelleted at 130 g×5 min and conditioned medium was used to dilute the cell suspension.

TABLE 103 List of cell lines used in the study Cat. Batch Cell density Cell line Supplier/Vendor Number Number (Cells/ml)* HL-60 ATCC/LCC CCL-240 63478792 15,000 MV4-11 ATCC/LCC CRL-9591 63567001 10,000 MOLM-13 AddexBio/DBA C003003  126132  1,000 * Cell density at seeding (T0) Test Item Stock Solution

TABLE 104 List of compounds tested External Compound ID MW MI-503 564.6 10 480.5 11 494.5 12 481.5 13 475.5

Test items were dissolved in glass vials at 10 mM in DMSO with purity ≥99.9% (Sigma, D8418, batch n. SHBH4245V) and stored at −20° C. in 1.5 mL Eppendorf tubes.

Compound Plate Preparation

Serial dilutions 1 to 3 in DMSO 100% were prepared starting from a 10 mM stock solutions to generate 7 points concentration response curve (CRC).

For each plate to test, one 0.4 μL copy plate and four 0.3 μL copy plates were then stamped into 96-well plates not treated for cell adhesion (Sarstedt-cat.no. 82.1581.001) by acoustic liquid Handling, Echo, at a concentration which was 500 fold the final assay concentration. Stamped plates were stored at −20° C. The final concentrations for the reference compound, MI-503, and the test items were: 2.00E-05, 6.67E-06, 2.22E-06, 7.41E-07, 2.47E-07, 8.23E-08 and 2.74E-08 M.

Long-Term Proliferation Assay Procedure

Cells were plated in 96-well flat bottom microtiter plates at cell density of 15,000 cells/ml for HL-60, 1000 cells/ml for MOLM-13 and 10,000 cell/ml for MV4-11. Cells were treated with 0.2% DMSO (Sigma, D8418, batch n. SHBH4245V) or serial dilutions of compounds (0.027 μM-20 μM) in DMSO (0.2% final concentration). Cells were incubated in a 5% CO₂ incubator at 37° C. for 4 days. A CellTiterGlo viability assay (Promega) was employed. Luminescence was read by using VictorV (Perkin Elmer) multilabel plate reader using the standard protocol for luminescence in 96 well plate. The experiment was performed in duplicate.

Data Handling and Analysis

Data were expressed as % of inhibition compared to the 0.2% DMSO negative control, and was calculated as follows: % inhibition=100−[(RLU sample)×100/(RLU average controls*)] *cells containing 0.2% DMSO

CRCs were analysed by GraphPad and IC₅₀ values were calculated by non-linear regression using 4 parameter-logistic equation. IC₅₀ (μM) values were reported in the final data table. The curve fittings were performed leaving free all the parameters. Any constrain were reported in the results table.

Results

After visual inspection no solubility issues were observed for all the compounds tested.

Increasing concentrations of MI-503 inhibited cell viability in a concentration dependent manner in all the cell lines treated with IC₅₀ values of 0.42 μM in HL-60, 0.19 μM in MV4-11 and 0.23 μM in MOLM-13 (FIG. 5 , FIG. 6 and FIG. 7 ).

As shown in Table 104, Compound 10 and Compound 11 inhibited the viability of MV4-11 and MOLM-13 with IC50 value of 0.22 μM and 0.2 μM, respectively in MV4-11 and 0.31 μM and 0.26 μM, respectively in MOLM-13. A similar effect was observed for both compounds in HL-60 cells with an IC50 of 0.36 μM for Compound 10 and 0.51 μM for Compound 11.

Also increasing concentrations of Compound 13 inhibited the cell viability of MV4-11 and MOLM-13 cells with IC₅₀ values of 0.91 μM and 1.23 μM, respectively. In HL-60, Compound 13 is slightly less potent with IC₅₀ of 2.75 μM (FIG. 5 , FIG. 6 and FIG. 7 ).

Compound 12 is not active up to the highest concentration tested in HL-60; slightly active in MOLM-13 cells with a maximal inhibition of about 40% and active in MV4-11 with an IC50 of 0.43 μM and a maximal inhibition of 89% (FIG. 5 , FIG. 6 and FIG. 7 ).

TABLE 104 Inhibitory effect of Compound 9, Compound 10, Compound 11, Compound 12, and Compound 13 and MI-503 on proliferation of MOLM-13, MV4-11 and HL-60 cells. HL-60 MV4-11 (MLL-AF4) MOLM-13 (MLL-AF9) IC₅₀ % IC₅₀ % IC₅₀ % # μM pIC₅₀ slope max μM pIC₅₀ slope max μM pIC₅₀ slope max  9 0.32 6.5 0.7  69 0.49 6.31 0.8 102 0.32 6.49 1.1  94 10 0.36 6.44 1.6  65 0.22 6.65 2.9 100 0.31 6.51 2.5  94 11 0.51 6.29 1.1 102 0.28 6.55 1.5 100 0.26 6.59 2.6  95 12 >20 <4.70 — — 0.43 6.37 4.1  89 ≈0.71 ≈6.15 13.1  42 13 2.75 5.56 1.1 112 0.91 6.04 1.1 105 1.23 5.91 1.4 101 MI- 0.42 6.38 1   103 0.19 6.73 1.4 100 0.23 6.63 1  98 503

Additional IC₅₀ data of representative compounds of invention in LTP Assay: Compound 11

Compound 11 IC₅₀ (μM) Cell Type T4 (Day 4) T7 T11 T14 HL-60 0.69  0.39 0.48 0.47 MOLM-13 (MLL-AF9) 0.66  0.513 0.32 0.42 MV4-11 (MLL-AF4) 0.65  0.50 0.42 0.31 RS4-11 (MLL-AF4) 1.23  0.85 0.11 ND Compound 11 showed a similar potency in all the cell lines tested with a slight increase in potency along the time in culture. Compound 12

Compound 12 IC₅₀ (μM) Cell Type T4 (Day 4) T7 T11 T14 HL-60 >5 >5 >5 >5 MOLM-13 (MLL-AF9) >5 5.75  0.562 >5 MV4-11 (MLL-AF4) 1.55 1.26  0.85 0.87 RS4-11 (MLL-AF4) 0.58 0.42  0.26 ND

At T4, increasing cone, of Compound 12 fully inhibits the cell viability of RS4;11. A partial effect was observed for MV4-11 and MOLM-13. No activity was observed in HL-60 up to the maximal cone. Tested.

Compound 19

Compound 19 IC₅₀ (μM) Cell Type T4 (Day 4) T7 T11 T14 HL-60 1.55 0.87 0.65 0.59 MOLM-13 (MLL-AF9) 0.83 0.74 0.78 1.32 MV4-11 (MLL-AF4) 1.29 1.41 0.05 0.08 RS4-11 (MLL-AF4) 1.62 1.55 >5 ND

At T4, increasing cone, of Compound 19 fully inhibits the cell viability of all the cells with an “all or none” response. The potency values obtained were estimated even if the slope was very high.

Compound 31

Compound 31 IC₅₀ (μM) Cell Type T4 (Day 4) T7 T11 T14 HL-60 >5 >5 >5 >5 MOLM-13 (MLL-AF9) >5 >5 >5 >5 MV4-11 (MLL-AF4) >5 >5 2.63 2.19 RS4-11 (MLL-AF4) >5 1.35 >5 ND

Compound 32 IC₅₀ (μM) Cell Type T4 (Day 4) T7 T11 T14 HL-60 >5 >5 >5 >5 MOLM-13 (MLL-AF9) >5 >5 >5 >5 MV4-11 (MLL-AF4) >5  4.905 3.09 2.69 RS4-11 (MLL-AF4) >5  2.75 >5 ND

Compound 33 IC₅₀ (μM) Cell Type T4 (Day 4) T7 T11 T14 HL-60 >5 >5 >5 >5 MOLM-13 (MLL-AF9) >5 >5 >5 >5 MV4-11 (MLL-AF4) >5 >5 3.31 2.34 RS4-11 (MLL-AF4) >5 >5 >5 ND Additional LTP Assay Data:

Compound 11 IC₅₀ (μM) Cell Type T4 (Day 4) T7 HL-60 0.692 0.389 MOLM-13 (MLL-AF9) 0.661 0.513 MV4-11 (MLL-AF4) 0.646 0.501 RS4-11 (MLL-AF4) 1.230 0.851

Compound 12 IC₅₀ (μM) Cell Type T4 (Day 4) T7 HL-60 >10 >10 MOLM-13 (MLL-AF9) >10 5.75 MV4-11 (MLL-AF4) 1.55 1.26 RS4-11 (MLL-AF4) 0.58 0.42

Compound 19 IC₅₀ (μM) Cell Type T4 (Day 4) T7 HL-60 1.55  0.871 MOLM-13 (MLL-AF9) 0.83  0.74 MV4-11 (MLL-AF4) 1.29  1.41 RS4-11 (MLL-AF4) 1.62  1.55 Conclusions

MI-503 showed potency values in line with data previously obtained.

InMV4-11, MOLM-13 and HL-6 0 cells, Compound 10, Compound 11 showed similar potency values; a similar profile was observed also for Compound 13 but with lowest potency values.

Compound 12 showed a peculiar profile. It fully inhibited the MV4-11 cell viability with a sub-micromolar potency. In MOLM-13 the compound is slightly active whereas completely inactive up to the highest concentration tested in HL-60.

Example 103: Alternate Long-Term Proliferation Assay Procedure

The day of the experiment (TO) all the cell line suspensions were counted by Cell Viability Analyser, Vi-CELL and properly diluted with fresh medium to obtain the cell density reported in the Test System paragraph.

Cells were tested after 4 passages after thawing.

200 μL/well and 150 μL/well of cell suspension were added into the 0.4 μL/well and 0.3 μL/well compound plates, respectively.

-   -   Cell plate containing 200 μL/well suspension was incubated at         37° C. in a humidified incubator with 5% CO₂.     -   From each well of the 150 μL/well cell assay plate, 100 μL were         harvested and transferred into a 96-well Optiplate (Perkin         Elmer, Cat. n. 6005290) and cell viability was measured as         described in 4.3 paragraphs (TO).

After four days in culture (T4) 150 μL/well of fresh medium were added into a new 0.3 μL/well copy compound plate.

-   -   From each well of the 200 μL/well cell assay plate:         -   100 μL were sampled for the cell viability measurement as             described in 4.3 paragraphs (T4).         -   50 μL were harvested and added to the 150 μL/well compound             plate prepared as described in the first point to dilute 1:4             the cell suspension.     -   The cell assay plate diluted and containing 200 μL/well         suspension were incubated at 37° C. in a humidified incubator         with 5% CO₂.

At T7-T11-T14 it was proceeded as described in T4, with the exception that no further cell dilution was carried out at T14.

Cell Viability Measurement

Plates containing the samples to be tested were equilibrated at room temperature for approximately 30 min and then 30 μL/well of the Promega CellTiterGlo® reagent were added.

Contents will be mixed for 5 min on an orbital shaker to induce cell lysis and then incubated at room temperature for an additional 10 min to stabilize the luminescent signal.

Luminescence was read by using VictorV (Perkin Elmer) multilabel plate reader using the standard protocol for luminescence in 96 well plate.

Data Handling and Analysis

Data were expressed as % of inhibition compared to the 0.2% DMSO negative control, and was calculated as follows: % inhibition=100−[(RLU sample)×100/(RLU average controls*)] *cells containing 0.2% DMSO

CRCs were analysed by GraphPad and IC₅₀ values were calculated by non-linear regression using 4 parameter-logistic equation. IC₅₀ (μM) values were reported in the final data table.

The curve fittings were performed leaving free all the parameters. Any constrain were reported in the results table.

Results

Cell Growth Curves

Cell growth curves were plotted as described in the experimental design session and reported in Appendix 1.

MOLM-13 and MV4-11 cells grew exponentially along the 14 days in culture with a growth rate cell type dependent.

HL-60 cells grew in an exponential manner up to 11 day in culture in both the experiments. A growth slowdown was observed between T11 and T14.

RS4; 11 cells showed a slow growth profile up to 7 days in culture followed by a progressive decrease of growth with a significant signal reduction at T14. At T14 the cell viability was very low close to the lower detection limit with the absence of a workable signal window. The data obtained at this time point (T14) were excluded from the data analysis.

Cell Proliferation Inhibition

A visual inspection of treated wells was carried out along the entire period of the treatment to assess whether compound precipitation occurred. No solubility issues were observed for any compound tested.

The effect of test substances to inhibit cell proliferation at different end points is summarized in FIG. 8 . pIC₅₀, IC₅₀, slope and % maximal effect at the highest tested concentration are reported.

MI-503—Increasing concentrations of MI-503 fully inhibited cell viability in a concentration dependent manner in all the cell lines treated with IC₅₀ values reported in FIG. 8 .

COMPOUND 11—Compound 11 fully inhibited cell viability in a concentration dependent manner with similar potency values in all the cell lines tested. A slight increase in potency along the time in culture was observed.

COMPOUND 12—At T4, increasing cone, of Compound 12 fully inhibited the cell viability of RS4; 11 cells. A partial effect was observed for MV4-11 and MOLM-13. No activity was observed in HL-60 up to the maximal cone, tested. The compound profile was confirmed more or less in all the time points with a weak leftward shift of the potency along the time in culture.

Example 201: Pharmaceutical Compositions

The compositions described below are presented with a compound of Formula (I)-(XXIIIh) for illustrative purposes.

Example 201a: Parenteral Composition

To prepare a parenteral pharmaceutical composition suitable for administration by injection, 100 mg of a water-soluble salt of a compound of Formula (I)-(XXIIIh) is dissolved in DMSO and then mixed with 10 mL of 0.9% sterile saline. The mixture is incorporated into a dosage unit form suitable for administration by injection.

Example 201b: Oral Composition

To prepare a pharmaceutical composition for oral delivery, 100 mg of a compound of Formula (I)-(XXIIIh) is mixed with 750 mg of starch. The mixture is incorporated into an oral dosage unit for, such as a hard gelatin capsule, which is suitable for oral administration.

Example 201c: Sublingual (Hard Lozenge) Composition

To prepare a pharmaceutical composition for buccal delivery, such as a hard lozenge, mix 100 mg of a compound of Formula (I)-(XXIIIh) with 420 mg of powdered sugar mixed, with 1.6 mL of light corn syrup, 2.4 mL distilled water, and 0.42 mL mint extract. The mixture is gently blended and poured into a mold to form a lozenge suitable for buccal administration.

Example 201d: Inhalation Composition

To prepare a pharmaceutical composition for inhalation delivery, 20 mg of a compound of Formula (I)-(XXIIIh) is mixed with 50 mg of anhydrous citric acid and 100 mL of 0.9% sodium chloride solution. The mixture is incorporated into an inhalation delivery unit, such as a nebulizer, which is suitable for inhalation administration.

Example 1 201e: Rectal Gel Composition

To prepare a pharmaceutical composition for rectal delivery, 100 mg of a compound of Formula (I)-(XXIIIh) is mixed with 2.5 g of methylcelluose (1500 mPa), 100 mg of methylparapen, 5 g of glycerin and 100 mL of purified water. The resulting gel mixture is then incorporated into rectal delivery units, such as syringes, which are suitable for rectal administration.

Example 201f: Topical Gel Composition

To prepare a pharmaceutical topical gel composition, 100 mg of a compound of Formula (I)-(XXIIIh) is mixed with 1.75 g of hydroxypropyl celluose, 10 mL of propylene glycol, 10 mL of isopropyl myristate and 100 mL of purified alcohol USP. The resulting gel mixture is then incorporated into containers, such as tubes, which are suitable for topical administration.

Example 201g: Ophthalmic Solution Composition

To prepare a pharmaceutical ophthalmic solution composition, 100 mg of a compound of Formula (I)-(XXIIIh) is mixed with 0.9 g of NaCl in 100 mL of purified water and filtered using a 0.2 micron filter. The resulting isotonic solution is then incorporated into ophthalmic delivery units, such as eye drop containers, which are suitable for ophthalmic administration.

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

At least some of the chemical names of compounds of the invention as given and set forth in this application, may have been generated on an automated basis by use of a commercially available chemical naming software program, and have not been independently verified In the instance where the indicated chemical name and the depicted structure differ, the depicted structure will control. In the chemical structures where a chiral center exists in a structure but no specific stereochemistry is shown for the chiral center, both enantiomers associated with the chiral structure are encompassed by the structure. 

What is claimed is:
 1. A method for treating diffuse large B cell lymphoma, follicular lymphoma, chronic lymphocytic leukemia, lymphoid leukemia, acute lymphoblastic lymphoma, soft tissue tumor, glioblastoma, pancreatic tumor, or renal cell cancer, comprising administering to a patient in need thereof a therapeutically effective amount of a compound of formula (I):

or a pharmaceutically acceptable salt thereof or pharmaceutical composition thereof, wherein: A is O, or N(R^(6a)); Cy is:

wherein R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur, phenyl, an 8-10 membered bicyclic aryl ring, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; one of X and Y is —NR^(3a)—; and the other is —C(R^(3b))₂—, —NR^(3b)—, or —O—; R¹ is an optionally substituted group selected from C₁₋₆ alkyl, C₃₋₇ cycloalkyl, phenyl, an 8-10 membered bicyclic aryl ring, a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; R² is H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, halo, or CN; each R³ª, and R^(3b) is independently H or C₁₋₆ alkyl; each R⁴ is independently H, halo, CN, OR, —N(R)₂, —C(O)N(R)₂, —NRC(O)R, —SO₂R, —C(O)R, —CO₂R, or an optionally substituted group selected from C₁₋₆ alkyl, C₃₋₇ cycloalkyl, a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, phenyl, an 8-10 membered bicyclic aryl ring, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; each R is independently H, or an optionally substituted group selected from C₁₋₆ aliphatic, phenyl, an 8-10 membered bicyclic aryl ring, a 4-7 membered saturated or partially unsaturated heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or: two R groups on the same nitrogen are taken together with their intervening atoms to form a 4-7 membered saturated, partially unsaturated, or heteroaryl ring having 0-3 heteroatoms, in addition to the nitrogen, independently selected from nitrogen, oxygen, or sulfur; R⁶ª is H or and C₁₋₆ alkyl; and n is 1, 2, 3, or 4, wherein the method for treating is a method for alleviating, abating or ameliorating symptoms of the disease or the condition; ameliorating underlying metabolic causes of the disease or the symptoms; inhibiting the disease or condition; arresting the development of the disease or condition; relieving the disease or condition; causing regression of the disease or condition; relieving a condition caused by the disease or condition; or stopping the symptoms of the disease or condition.
 2. The method according to claim 1, wherein the compound is according to formula (IVa), (IVb), (IVc), (IVd), (Va), (Vb), (Vc) or (Vd):

or a pharmaceutically acceptable salt thereof, wherein: R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
 3. The method according to claim 1, wherein the compound is according to formula (VIa′), (VIb′), (VIc′), (VId′), (VIIa′), (VIIb′), (VIIc′) or (VIId′):

or a pharmaceutically acceptable salt thereof; wherein: R⁷ is an optionally substituted group selected from a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
 4. The method according to claim 1, wherein R¹ is phenyl, pyrrolyl, furanyl, thienyl, pyrazolyl, imidazolyl, oxazolyl, isoxazolyl, thiazolyl, triazolyl, thiadiazolyl, pyridyl, pyrimidinyl, or pyrazinyl, wherein each is unsubstituted, or substituted with Me, Et, i-Pr, OMe, CF₃, F, Cl, and CN.
 5. The method according to claim 1, wherein R⁷ is a 4-7 membered heterocycloalkyl ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur substituted with Me, Et, or i-Pr.
 6. The method according to claim 1, wherein R⁷ is substituted or unsubstituted pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, pyridyl, pyrrolyl, pyrazolyl, imidazolyl, oxazolyl, triazolyl, thiazolyl, oxadiazolyl, or thiadiazolyl.
 7. The method according to claim 1, wherein R⁷ is morpholinyl.
 8. The method according to claim 1, wherein R⁷ is imidazolyl substituted with Me, Et, i-Pr, Cl, F, CF₃, or CN.
 9. The method according to claim 1, wherein the compound is according to formula (VIIIa), (VIIIb), (VIIIc), (VIIId), (IXa), (IXb), (IXc) or (IXd):

or a pharmaceutically acceptable salt thereof.
 10. The method according to claim 1, wherein the compound is according to formula (Xa), (Xb), (Xc), (Xd), (Xe), (Xf), (Xg), (Xh), (XIa), (XIb), (XIc), (XId), (XIe), (XIf), (XIg) or (XIh):

or a pharmaceutically acceptable salt thereof.
 11. The method according to claim 1, wherein the compound is according to formula (XIIa), (XIIb), (XIIc), (XIId), (XIIIa), (XIIIb), (XIIIc) or (XIIId):

or a pharmaceutically acceptable salt thereof.
 12. The method according to claim 1, wherein the compound is according to formula (XIVa), (XIVb), (XIVc), (XIVd), (XIVe), (XIVf), (XIVg) or (XIVh), (XVa), (XVb), (XVc), (XVd)), (XVe), (XVf), (XVg) or (XVh):

or a pharmaceutically acceptable salt thereof.
 13. The method according to claim 1, wherein the compound is according to formula (XVIa), (XVIb), (XVIc), (XVId), (XVIIa), (XVIIb), (XVIIc) or (XVIId):

or a pharmaceutically acceptable salt thereof.
 14. The method according to claim 1, wherein the compound is according to formula (XVIIIa), (XVIIIb), (XVIIIc), (XVIIId), (XVIIIe), (XVIIIf), (XVIIIg), (XVIIIh) (XIXa), (XIXb), (XIXc), (XIXd), (XIXe), (XIXf), (XIXg) or (XIXh):

or a pharmaceutically acceptable salt thereof.
 15. The method according to claim 1, wherein the compound is according to formula (XXa), (XXb), (XXc), (XXd), (XXIa), (XXIb), (XXIc) or (XXId):

or a pharmaceutically acceptable salt thereof.
 16. The method according to claim 1, wherein the compound is according to formula (XXIIa), (XXIIb), (XXIIc), (XXIId), (XXIIe), (XXIf), (XXIIg), (XXIIh), (XXIIIa), (XXIIIb) (XXIIIc), (XXIIId), (XXIIIe), (XXIIIf), (XXIIIg) or (XXIIIh):

or a pharmaceutically acceptable salt thereof.
 17. The method according to claim 1, wherein the compound is according to formula (VIIb), (VIIIb), (XIVb), or (XIVf):

or a pharmaceutically acceptable salt thereof.
 18. The method according to claim 1, wherein the compound is selected from any one of the following compounds, or a pharmaceutically acceptable salt thereof:


19. The method according to claim 1, wherein in the compound of formula (I) or the pharmaceutically acceptable salt thereof or pharmaceutical composition thereof: A is O, or N(R^(6a)); Cy is:

wherein R⁷ is

one of X and Y is —NR^(3a)—; and the other is —C(R^(3b))₂—, or —NR^(3b)—; R¹ is an optionally substituted group selected from a 5-6 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; R² is H, or C₁₋₆ alkyl; each R³ª, and R^(3b) is independently H; each R⁴ is independently H, C₁₋₆ alkyl; R⁶ª is H or C₁₋₆ alkyl; and n is 1, 2, 3, or
 4. 20. The method according to claim 19, wherein the compound is selected from any one of the following compounds, or a pharmaceutically acceptable salt thereof: 